40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2010 CFR

2010-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2014 CFR

2014-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2012 CFR

2012-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2010 CFR

2010-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2011 CFR

2011-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2013 CFR

2013-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2012 CFR

2012-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2013 CFR

2013-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2014 CFR

2014-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2011 CFR

2011-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

Landuse legacies of old-field succession and soil structure at the Calhoun Criticl Zone Observatory in SC, USA.

NASA Astrophysics Data System (ADS)

Brecheisen, Z. S.; Richter, D. D., Jr.; Callaham, M.; Carrera-Martinez, R.; Heine, P.

2017-12-01

The pre-colonial Southern Piedmont was an incredibly stable CZ with erosion rates between 0.35-3m/Myr on a 4th order interfluve. With soils and saprolite weathered up to 30m in total depth bedrock with multi-million year residence times under continual forest cover prior to widespread agricultural disturbance. With this biogeomorphic stability came time for soil macroporosity and soil structure to be established and maintained by the activities of soil fauna, plant root growth and death, and tree-fall tip-up events serving to continually mix and aerate the soil. Greatly accelerated surficial agricultural erosion (ca. 1750-1930) has fundamentally altered the Calhoun Critical Zone Observatory forest community dynamics aboveground and the soil structure, hydrology, and biogeochemistry belowground. The arrival of the plow to the Southern Piedmont marked the destruction of soil structure, macropore networks, and many of the macroinvertebrate soil engineers. This transformation came via forest clearing, soil tilling, compaction, and wholesale soil erosion, with the region having lost an estimated average of 18cm of soil across the landscape. In the temporal LULC progression from hardwood forests, to cultivated farms, to reforestation, secondary forest soil structure is expected to remain altered compared to the reference hardwood ecosystems. The research presented herein seeks to quantify CZ soil structure regeneration in old-field pine soil profiles' Ksat, aggregation, texture, macro-invertebrates, and direct measurements of topsoil porosity using X-ray computed tomography analysis on 15cm soil cores.

Method for analyzing soil structure according to the size of structural elements

NASA Astrophysics Data System (ADS)

Wieland, Ralf; Rogasik, Helmut

2015-02-01

The soil structure in situ is the result of cropping history and soil development over time. It can be assessed by the size distribution of soil structural elements such as air-filled macro-pores, aggregates and stones, which are responsible for important water and solute transport processes, gas exchange, and the stability of the soil against compacting and shearing forces exerted by agricultural machinery. A method was developed to detect structural elements of the soil in selected horizontal slices of soil core samples with different soil structures in order for them to be implemented accordingly. In the second step, a fitting tool (Eureqa) based on artificial programming was used to find a general function to describe ordered sets of detected structural elements. It was shown that all the samples obey a hyperbolic function: Y(k) = A /(B + k) , k ∈ { 0 , 1 , 2 , … }. This general behavior can be used to develop a classification method based on parameters {A and B}. An open source software program in Python was developed, which can be downloaded together with a selection of soil samples.

Testing the Visual Soil Assessment tool on Estonian farm fields

NASA Astrophysics Data System (ADS)

Reintam, Endla; Are, Mihkel; Selge, Are

2017-04-01

Soil quality estimation plays important role in decision making on farm as well on policy level. Sustaining the production ability and good health of the soil the chemical, physical and biological indicators should be taken into account. The system to use soil chemical parameters is usually quite well established in most European counties, including Estonia. However, measuring soil physical properties, such bulk density, porosity, penetration resistance, structural stability ect is time consuming, needs special tools and is highly weather dependent. In that reason these parameters are excluded from controllable quality parameters in policy in Estonia. Within the project "Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience" (iSQAPER) the visual soil assessment (VSA) tool was developed for easy detection of soil quality as well the different soil friendly agricultural management practices (AMP) were detected. The aim of current study was to test the VSA tool on Estonian farm fields under different management practices and compare the results with laboratory measurements. The main focus was set on soil physical parameters. Next to the VSA, the undisturbed soil samples were collected from the depth of 5-10 cm and 25-30 cm. The study revealed that results of a visually assessed soil physical parameters, such a soil structure, soil structural stability, soil porosity, presence of tillage pan, were confirmed by laboratory measurements in most cases. Soil water stable structure measurement on field (on 1 cm2 net in one 1 l box with 4-6 cm air dry clods for 5-10 min) underestimated very well structured soil on grassland and overestimated the structure aggregates stability of compacted soil. The slightly better soil quality was detected under no-tillage compared to ploughed soils. However, the ploughed soil got higher quality points compared with minimum tillage. The slurry application (organic manuring) had controversial impact - it increased the number of earthworms but decreased soil structural stability. Even the manuring with slurry increases organic matter amount in the soil, the compaction due to the use of heavy machinery during the application, especially on wet soil, reduces the positive effect of slurry.

Soil-Structural Stability as Affected by Clay Mineralogy, Soil Texture and Polyacrylamide Application

USDA-ARS?s Scientific Manuscript database

Soil-structural stability (expressed in terms of aggregate stability and pore size distribution) depends on (i) soil inherent properties, (ii) extrinsic condition prevailing in the soil that may vary temporally and spatially, and (iii) addition of soil amendments. Different soil management practices...

Influence of soil structure on nutrient cycling using microfluidic techniques

NASA Astrophysics Data System (ADS)

Arellano Caicedo, Carlos; Aleklett, Kristin; Ohlsson, Pelle; Hammer, Edith

2017-04-01

The rising of atmospheric CO2 levels and its effects on global warming make it necessary to understand the elements that regulate such levels and furthermore try to slow down the CO2 accumulation in the atmosphere. The exchange of carbon between soil and atmosphere plays a significant role in the atmospheric carbon budget. Soil organisms deposit organic compounds on and in soil aggregates, either as exudates or dead remains. Much of this dead organic material is quickly recycled, but a portion, however, will stay in the soil for long term. Evidence suggests that micro-scale biogeochemical interactions could play a highly significant role in degradation or persistence of organic matter in soils, thus, soil physical structure might play a decisive role in preventing accessibility of nutrients to microorganisms. For studying effects of spatial microstructure on soil nutrient cycles, we have constructed artificial habitats for microbes that simulate soil structures. Microfluidic, so called Lab-on-a-chip technologies, are one of the tools used to achieve our purpose. Such micro-habitats consist of pillar structures of difference density and surface area, tunnels with increasing depth, and mazes of increasing complexity to simulate different stages of soil aggregation. Using microscopy and analytical chemistry, we can follow the growth of microorganisms inoculated into the "soil chip" as well as the chemical degradation of organic matter compounds provided as nutrient source. In this way, we want to be able to predict how soil structure influences soil microbial activity leading to different effects on the carbon cycle. Our first results of a chip inoculated with natural soil showed a succession of organisms colonizing channels leading to dead-end arenas, starting with a high presence of bacteria inside the chip during the first days. Fungal hyphae growth gradually inside the channels until it finally occupied the big majority of the spaces isolating bacteria which dramatically decreased in number. The structure inside the soil chip changes dynamically due to the creation of biofilms. Such changes alter the spatial distribution inside the chip gradually, to the point of getting significantly different from the original structures. Fungal hyphae, bacterial biofilms, and microbial necro mass accumulation where the components altering the chip structure. These findings suggest that a considerable part of the soil structure is microbial biomass. Using Lab-on-a-chip techniques leads to the creation of a much more realistic soil and ecosystem model, resembling spatial and chemical complexity in real soil structures at a micrometer scale, the scale relevant for soil organisms. Understanding small-scale processes in the soils is crucial to predict carbon and nutrient cycling, and to enable us to give recommendations for soil management in agriculture, horticulture and nature conservation. If parameterization of soil structure as a central determinant for carbon sequestration is possible, it will allow strong argumentation for management practices that conserve and foster soil structure, such as low-tillage, support of mycorrhizal fungi, and reduction of heavy machinery usage.

Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils

PubMed Central

Delgado-Balbuena, Laura; Bello-López, Juan M.; Navarro-Noya, Yendi E.; Rodríguez-Valentín, Analine; Luna-Guido, Marco L.; Dendooven, Luc

2016-01-01

Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the effect of application of carrot residue, earthworms or the surfactant on the bacterial community structure was more accentuated in the arable soil than in the pasture soil. It was found that removal of anthracene was not linked to changes in the bacterial community structure. PMID:27727277

Interactions between soil texture, water, and nutrients control patterns of biocrusts abundance and structure

NASA Astrophysics Data System (ADS)

Young, Kristina; Bowker, Matthew; Reed, Sasha; Howell, Armin

2017-04-01

Heterogeneity in the abiotic environment structures biotic communities by controlling niche space and parameters. This has been widely observed and demonstrated in vascular plant and other aboveground communities. While soil organisms are presumably also strongly influenced by the physical and chemical dimensions of the edaphic environment, there are fewer studies linking the development, structure, productivity or function of surface soil communities to specific edaphic gradients. Here, we use biological soil crusts (biocrusts) as a model system to determine mechanisms regulating community structure of soil organisms. We chose soil texture to serve as an edaphic gradient because of soil texture's influence over biocrust distribution on a landscape level. We experimentally manipulated texture in constructed soil, and simultaneously manipulated two main outcomes of texture, water and nutrient availability, to determine the mechanism underlying texture's influence on biocrust abundance and structure. We grew biocrust communities from a field-sourced inoculum on four different soil textures, sieved from the same parent soil material, manipulating watering levels and nutrient additions across soil textures in a full-factorial design over a 5-month period of time. We measured abundance and structure of biocrusts over time, and measured two metrics of function, N2 fixation rates and soil stabilization, at the conclusion of the experiment. Our results showed finer soil textures resulted in faster biocrust community development and dominance by mosses, whereas coarser textures grew more slowly and had biocrust communities dominated by cyanobacteria and lichen. Additionally, coarser textured soils contained cyanobacterial filaments significantly deeper into the soil profile than fine textured soils. N2-fixation values increased with increasing moss cover and decreased with increasing cyanobacterial cover, however, the rate of change depended on soil texture and water amount. Soil shear resistance was highest on finer textured soil with the highest watering treatment, whereas compression resistance was highest on the coarsest textured soils with the highest watering amounts. Nutrient addition did not influence total cover or biocrust function, but did decrease lichen cover. Taken together, these results suggest that interactions between soil texture, water, and to a lesser degree nutrients, create predictable patterns in biocrust assemblage and offers a mechanistic understanding of edaphic controls over biocrust abundance and structure. These insights add to our increasing understanding of how edaphic gradients structure soil communities.

Land-use change and soil type are drivers of fungal and archaeal communities in the Pampa biome.

PubMed

Lupatini, Manoeli; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Suleiman, Afnan Khalil Ahmad; Fulthorpe, Roberta R; Roesch, Luiz Fernando Würdig

2013-02-01

The current study aimed to test the hypothesis that both land-use change and soil type are responsible for the major changes in the fungal and archaeal community structure and functioning of the soil microbial community in Brazilian Pampa biome. Soil samples were collected at sites with different land-uses (native grassland, native forest, Eucalyptus and Acacia plantation, soybean and watermelon field) and in a typical toposequence in Pampa biome formed by Paleudult, Albaqualf and alluvial soils. The structure of soil microbial community (archaeal and fungal) was evaluated by ribosomal intergenic spacer analysis and soil functional capabilities were measured by microbial biomass carbon and metabolic quotient. We detected different patterns in microbial community driven by land-use change and soil type, showing that both factors are significant drivers of fungal and archaeal community structure and biomass and microbial activity. Fungal community structure was more affected by land-use and archaeal community was more affected by soil type. Irrespective of the land-use or soil type, a large percentage of operational taxonomic unit were shared among the soils. We accepted the hypothesis that both land-use change and soil type are drivers of archaeal and fungal community structure and soil functional capabilities. Moreover, we also suggest the existence of a soil microbial core.

Topsoil structure stability in a restored floodplain: Impacts of fluctuating water levels, soil parameters and ecosystem engineers.

PubMed

Schomburg, A; Schilling, O S; Guenat, C; Schirmer, M; Le Bayon, R C; Brunner, P

2018-10-15

Ecosystem services provided by floodplains are strongly controlled by the structural stability of soils. The development of a stable structure in floodplain soils is affected by a complex and poorly understood interplay of hydrological, physico-chemical and biological processes. This paper aims at analysing relations between fluctuating groundwater levels, soil physico-chemical and biological parameters on soil structure stability in a restored floodplain. Water level fluctuations in the soil are modelled using a numerical surface-water-groundwater flow model and correlated to soil physico-chemical parameters and abundances of plants and earthworms. Causal relations and multiple interactions between the investigated parameters are tested through structural equation modelling (SEM). Fluctuating water levels in the soil did not directly affect the topsoil structure stability, but indirectly through affecting plant roots and soil parameters that in turn determine topsoil structure stability. These relations remain significant for mean annual days of complete and partial (>25%) water saturation. Ecosystem functioning of a restored floodplain might already be affected by the fluctuation of groundwater levels alone, and not only through complete flooding by surface water during a flood period. Surprisingly, abundances of earthworms did not show any relation to other variables in the SEM. These findings emphasise that earthworms have efficiently adapted to periodic stress and harsh environmental conditions. Variability of the topsoil structure stability is thus stronger driven by the influence of fluctuating water levels on plants than by the abundance of earthworms. This knowledge about the functional network of soil engineering organisms, soil parameters and fluctuating water levels and how they affect soil structural stability is of fundamental importance to define management strategies of near-natural or restored floodplains in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

An examination of the earthquake behaviour of a retaining wall considering soil-structure interaction

NASA Astrophysics Data System (ADS)

Köktan, Utku; Demir, Gökhan; Kerem Ertek, M.

2017-04-01

The earthquake behavior of retaining walls is commonly calculated with pseudo static approaches based on Mononobe-Okabe method. The seismic ground pressure acting on the retaining wall by the Mononobe-Okabe method does not give a definite idea of the distribution of the seismic ground pressure because it is obtained by balancing the forces acting on the active wedge behind the wall. With this method, wave propagation effects and soil-structure interaction are neglected. The purpose of this study is to examine the earthquake behavior of a retaining wall taking into account the soil-structure interaction. For this purpose, time history seismic analysis of the soil-structure interaction system using finite element method has been carried out considering 3 different soil conditions. Seismic analysis of the soil-structure model was performed according to the earthquake record of "1971, San Fernando Pacoima Dam, 196 degree" existing in the library of MIDAS GTS NX software. The results obtained from the analyses show that the soil-structure interaction is very important for the seismic design of a retaining wall. Keywords: Soil-structure interaction, Finite element model, Retaining wall

High Energy Moisture Characteristics: Linking Between Soil Physical Processes and Structure Stability

USDA-ARS?s Scientific Manuscript database

Water storage and flow in soils is usually complicated by the intricate nature of and changes in soil pore size distribution (PSD) due to modifications in soil structure following changes in agricultural management. The paper presents the Soil High Energy Moisture Characteristic (Soil-HEMC) method f...

A long-term soil structure observatory for post-compaction soil structure evolution: design and initial soil structure recovery observations

NASA Astrophysics Data System (ADS)

Keller, Thomas; Colombi, Tino; Ruiz, Siul; Grahm, Lina; Reiser, René; Rek, Jan; Oberholzer, Hans-Rudolf; Schymanski, Stanislaus; Walter, Achim; Or, Dani

2016-04-01

Soil compaction due to agricultural vehicular traffic alters the geometrical arrangement of soil constituents, thereby modifying mechanical properties and pore spaces that affect a range of soil hydro-ecological functions. The ecological and economic costs of soil compaction are dependent on the immediate impact on soil functions during the compaction event, and a function of the recovery time. In contrast to a wealth of soil compaction information, mechanisms and rates of soil structure recovery remain largely unknown. A long-term (>10-yr) soil structure observatory (SSO) was established in 2014 on a loamy soil in Zurich, Switzerland, to quantify rates and mechanisms of structure recovery of compacted arable soil under different post-compaction management treatments. We implemented three initial compaction treatments (using a two-axle agricultural vehicle with 8 Mg wheel load): compaction of the entire plot area (i.e. track-by-track), compaction in wheel tracks, and no compaction. After compaction, we implemented four post-compaction soil management systems: bare soil (BS), permanent grass (PG), crop rotation without mechanical loosening (NT), and crop rotation under conventional tillage (CT). BS and PG provide insights into uninterrupted natural processes of soil structure regeneration under reduced (BS) and normal biological activity (PG). The two cropping systems (NT and CT) enable insights into soil structure recovery under common agricultural practices with minimal (NT) and conventional mechanical soil disturbance (CT). Observations include periodic sampling and measurements of soil physical properties, earthworm abundance, crop measures, electrical resistivity and ground penetrating radar imaging, and continuous monitoring of state variables - soil moisture, temperature, CO2 and O2 concentrations, redox potential and oxygen diffusion rates - for which a network of sensors was installed at various depths (0-1 m). Initial compaction increased soil bulk density to about half a metre, decreased gas and water transport functions (air permeability, gas diffusivity, saturated hydraulic conductivity), and increased mechanical impedance. Water infiltration at the soil surface was initially reduced by three orders of magnitude, but significantly recovered within a year. However, within the soil profile, recovery of transport properties is much smaller. Air permeability tended to recover more than gas diffusivity, suggesting that initial post-compaction recovery is initiated by new macropores (e.g. biopores). Tillage recovered topsoil bulk density but not topsoil transport functions. Compaction changed grass species composition in PG, and significantly reduced grass biomass in PG and crop yields in NT and CT.

The Vertical Structure of Urban Soils and Their Convergence Across Cities

EPA Science Inventory

The theoretical patterns for vertical soil structure (e.g., A-B-C ordering of horizons) are a basis for research methods and our understanding of ecosystem structure and function in general. A general understanding of how urban soils differ from non-urban soils vertically is need...

[Effects of Phyllostachys edulis cultivation on soil bacterial and fungal community structure and diversity].

PubMed

Zhao, Tian Xin; Mao, Xin Wei; Cheng, Min; Chen, Jun Hui; Qin, Hua; Li, Yong Chun; Liang, Chen Fei; Xu, Qiu Fang

2017-11-01

This study examined how soil bacterial and fungal communities responded to the cultivation history of Moso bamboo in Anji and Changxing counties, Huzhou, Zhejiang, China. Soil samples (0-20 and 20-40 cm) were taken from bamboo plantations subjected to different cultivation histories and analyzed the community structures of soil bacterial and fungal by PCR-DGGE methods. It was found that soil bacterial and fungal communities varied greatly with the development of bamboo plantations which converted from Masson pine forest or formed via invading adjacent broadleaf shrub forest. Soil bacterial community structures exhibited a greater response to bamboo cultivation time than fungal community, but bacteria structure of surface soil displayed an ability of resiliency to disturbance and the tendency to recover to the original state. The cultivation time, sampling site and soil layer significantly affected the biodiversity of soil bacteria and fungi, especially the latter two factors. Redundancy analysis (RDA) of soil properties and bacteria or fungi communities showed that there were no accordant factors to drive the alteration of microbial structure, and the first two axes explained less than 65.0% of variance for most of the sampling sites and soil layers, indicating there existed soil parameters besides the five examined that contributed to microbial community alteration.

Agriculturization in the Argentinean Northern Humid Pampas: the Impact on Soil Structure and Runoff

NASA Astrophysics Data System (ADS)

Sasal, M. C.; Léonard, J.; Andriulo, A.; Wilson, M. G.

2012-04-01

Argentina is among the countries with the largest cropped area under no-tillage (NT). No tillage was adopted in the northern Humid Pampas to reduce the widespread soil degradation by water erosion. With the advent of genetically modified soybean varieties, NT has developed exponentially. This evolution, combined with the influence of the international market trend, has resulted in large changes in crop sequence composition toward the disappearance of pastures and the expansion of soybean monoculture. The aim of this work was to evaluate the long-term consequences of these changes on the topsoil structure and the way in which the evolution of soil structure relates to the simplification of the crop sequence and to runoff at a regional scale. We analyzed the topsoil structure of 25 sites with Argiudolls having 4 to 29 consecutive years of NT using the cultural profile approach. An intensification sequence index (ISI) was calculated as the ratio between the length of the growth period and the length of the year. Fifteen natural-rainfall runoff plots (100 m2) with 3.5% slope were used to analyze the relationship between soil structural state, crop sequence and runoff for four years. Four types of soil structures were identified and a general pattern of vertical soil structure organization was revealed. The top centimeters of 72% of the sites were dominated by a granular structure. Platy soil structure development was omnipresent: all sites exhibited a horizontal platy structure (<10 cm thick) developing either directly from the soil surface or from below the granular structure. Below the platy structure layer, a gamma soil structure (with visible structural porosity) was observed in all sites (30-75% of the A horizon), while compacted delta soil structure was detected in localized zones. A significant parabolic relationship (R2=0.60) was found between the number of consecutive years under NT and the proportion of platy structure in the A horizon. The proportion of platy structure increased during the first 15 years of NT, and then the extension of platy structure tended to stabilize and even to decrease after 20 to 25 years. The development of platy soil structure was negatively related to the ISI (R2=0.57) and runoff increased as the proportion of platy structure increased and the proportion of granular structure decreased (R2=0.85). We concluded that high soybean frequency in cropping systems under NT favors the extension of platy soil structure and increases runoff. More than 70% of the agricultural area of the northern Humid Pampas region is currently covered by soybean cultivation, mostly as a single annual crop (ISI=0.38). Our results thus suggest that promoting management practices such as the expansion of wheat/soybean double crop (ISI=0.83) could limit soil structure degradation and reduce runoff and the associated environmental risks.

Modeling the Dynamics of Soil Structure and Water in Agricultural Soil

NASA Astrophysics Data System (ADS)

Weller, U.; Lang, B.; Rabot, E.; Stössel, B.; Urbanski, L.; Vogel, H. J.; Wiesmeier, M.; Wollschlaeger, U.

2017-12-01

The impact of agricultural management on soil functions is manifold and severe. It has both positive and adverse influence. Our goal is to develop model tools quantifying the agricultural impact on soil functions based on a mechanistic understanding of soil processes to support farmers and decision makers. The modeling approach is based on defining relevant soil components, i.e. soil matrix, macropores, organisms, roots and organic matter. They interact and form the soil's macroscopic properties and functions including water and gas dynamics, and biochemical cycles. Based on existing literature information we derive functional interaction processes and combine them in a network of dynamic soil components. In agricultural soils, a major issue is linked to changes in soil structure and their influence on water dynamics. Compaction processes are well studied in literature, but for the resilience due to root growth and activity of soil organisms the information is scarcer. We implement structural dynamics into soil water and gas simulations using a lumped model that is both coarse enough to allow extensive model runs while still preserving some important, yet rarely modeled phenomenons like preferential flow, hysteretic and dynamic behavior. For simulating water dynamics, at each depth, the model assumes water at different binding energies depending on soil structure, i.e. the pore size distribution. Non-equilibrium is postulated, meaning that free water may occur even if the soil is not fully saturated. All energy levels are interconnected allowing water to move, both within a spatial node, and between neighboring nodes (adding gravity). Structure dynamics alters the capacity of this water compartments, and the conductance of its connections. Connections are switched on and off depending on whether their sources contain water or their targets have free capacity. This leads to piecewise linear system behavior that allows fast calculation for extended time steps. Based on this concept, the dynamics of soil structure can be directly linked to soil water dynamics as a main driver for other soil processes. Further steps will include integration of temperature and solute leaching as well as defining the feedback of the water regime on the structure forming processes.

Impact of roots, mycorrhizas and earthworms on soil physical properties as assessed by shrinkage analysis

NASA Astrophysics Data System (ADS)

Milleret, R.; Le Bayon, R.-C.; Lamy, F.; Gobat, J.-M.; Boivin, P.

2009-07-01

SummarySoil biota such as earthworms, arbuscular mycorrhizal fungi (AMF) and plant roots are known to play a major role in engineering the belowground part of the terrestrial ecosystems, thus strongly influencing the water budget and quality on earth. However, the effect of soil organisms and their interactions on the numerous soil physical properties to be considered are still poorly understood. Shrinkage analysis allows quantifying a large spectrum of soil properties in a single experiment, with small standard errors. The objectives of the present study were, therefore, to assess the ability of the method to quantify changes in soil properties as induced by single or combined effects of leek roots ( Allium porrum), AMF ( Glomus intraradices) and earthworms ( Allolobophora chlorotica). The study was performed on homogenised soil microcosms and the experiments lasted 35 weeks. The volume of the root network and the external fungal hyphae was measured at the end, and undisturbed soil cores were collected. Shrinkage analysis allowed calculating the changes in soil hydro-structural stability, soil plasma and structural pore volumes, soil bulk density and plant available water, and structural pore size distributions. Data analysis revealed different impacts of the experimented soil biota on the soil physical properties. At any water content, the presence of A. chlorotica resulted in a decrease of the specific bulk volume and the hydro-structural stability around 25%, and in a significant increase in the bulk soil density. These changes went with a decrease of the structural pore volumes at any pore size, a disappearing of the thinnest structural pores, a decrease in plant available water, and a hardening of the plasma. On the contrary, leek roots decreased the bulk soil density up to 1.23 g cm -3 despite an initial bulk density of 1.15 g cm -3. This increase in volume was accompanied with a enhanced hydro-structural stability, a larger structural pore volume at any pore size, smaller structural pore radii and an increase in plant available water. Interestingly, a synergistic effect of leek roots and AMF in the absence of the earthworms was highlighted, and this synergistic effect was not observed in presence of earthworms. The structural pore volume generated by root and AMF growth was several orders of magnitude larger than the volume of the organisms. Root exudates as well as other AMF secretion have served as carbon source for bacteria that in turn would enhance soil aggregation and porosity, thus supporting the idea of a self-organization of the soil-plant-microbe complex previously described.

Soil structure characterized using computed tomographic images

Treesearch

Zhanqi Cheng; Stephen H. Anderson; Clark J. Gantzer; J. W. Van Sambeek

2003-01-01

Fractal analysis of soil structure is a relatively new method for quantifying the effects of management systems on soil properties and quality. The objective of this work was to explore several methods of studying images to describe and quantify structure of soils under forest management. This research uses computed tomography and a topological method called Multiple...

Afforestation alters community structure of soil fungi.

PubMed

Carson, Jennifer K; Gleeson, Deirdre B; Clipson, Nicholas; Murphy, Daniel V

2010-07-01

Relatively little is known about the effect of afforestation on soil fungal communities. This study demonstrated that afforestation altered fungal community structure and that changes were correlated to pools of soil C. Pasture at three locations on the same soil type was afforested with Eucalyptus globulus or Pinus pinaster. The structure of fungal communities under the three land uses was measured after 13y using automated ribosomal intergenic spacer analysis (ARISA). Afforestation significantly altered the structure of fungal communities. The effect of location on the structure of fungal communities was limited to pasture soils; although these contained the same plant species, the relative composition of each species varied between locations. Differences in the structure of fungal communities between pasture, E. globulus and P. pinaster were significantly correlated with changes in the amount of total organic C and microbial biomass-C in soil. Afforestation of patches of agricultural land may contribute to conserving soil fungi in agricultural landscapes by supporting fungal communities with different composition to agricultural soils. Copyright © 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Soil compaction--indicators for the assessment of harmful changes to the soil in the context of the German Federal Soil Protection Act.

PubMed

Lebert, Matthias; Böken, Holger; Glante, Frank

2007-02-01

Soil compaction in agriculture induced by large-scale equipment is of growing concern. Heavy wheel loads used in arable cropping have the potential to cause irreversible damage to the subsoil structure and may lead to harmful soil compaction. In order to sustain or improve soil health or fitness on a sustainable basis, indicators are needed to assess the changes in the soil structure and the respective soil functions. This requires an adequate verification of methods for distinguishing between the impairment of soil structure and the disruption of soil functions, and for the respective subject of protection. In this article the link between existing models of soil physical prognosis, practical guidelines, and criteria for the identification of affected soil structure is demonstrated, and a viable concept to distinguish harmful changes to the soil is presented. The concept consists of methods for soil physical analysis such as "pre-compression stress" and "loading ratio", practical recommendations for best management practice, and an indicator-based model for the identification of harmful subsoil compaction derived from a research project for the German Federal Environmental Agency, making it possible to determine for a respective location the required level of action far beyond the common practice of precautions against harmful soil compaction.

Colonization and community structure of root-associated microorganisms of Sabina vulgaris with soil depth in a semiarid desert ecosystem with shallow groundwater.

PubMed

Taniguchi, Takeshi; Usuki, Hiroyuki; Kikuchi, Junichi; Hirobe, Muneto; Miki, Naoko; Fukuda, Kenji; Zhang, Guosheng; Wang, Linhe; Yoshikawa, Ken; Yamanaka, Norikazu

2012-08-01

Arbuscular mycorrhizal fungi (AMF) have been observed in deep soil layers in arid lands. However, change in AMF community structure with soil depth and vertical distributions of the other root-associated microorganisms are unclear. Here, we examined colonization by AMF and dark septate fungi (DSF), as well as the community structure of AMF and endophytic fungi (EF) and endophytic bacteria (EB) in association with soil depth in a semiarid desert with shallow groundwater. Roots of Sabina vulgaris and soils were collected from surface to groundwater level at 20-cm intervals. Soil chemistry (water content, total N, and available P) and colonization of AMF and DSF were measured. Community structures of AMF, EF, and EB were examined by terminal restriction fragment length polymorphism analysis. AMF colonization decreased with soil depth, although it was mostly higher than 50%. Number of AMF phylotypes decreased with soil depth, but more than five phylotypes were observed at depths up to 100 cm. Number of AMF phylotypes had a significant and positive relationship with soil moisture level within 0-15% of soil water content. DSF colonization was high but limited to soil surface. Number of phylotypes of EF and EB were diverse even in deep soil layers, and the community composition was associated with the colonization and community composition of AMF. This study indicates that AMF species richness in roots decreases but is maintained in deep soil layers in semiarid regions, and change in AMF colonization and community structure associates with community structure of the other root-associated microorganisms.

The physico-chemical properties and structural characteristics of artificial soil for cut slope restoration in Southwestern China

PubMed Central

Chen, Shunan; Ai, Xiaoyan; Dong, Tengyun; Li, Binbin; Luo, Ruihong; Ai, Yingwei; Chen, Zhaoqiong; Li, Chuanren

2016-01-01

Cut slopes are frequently generated by construction work in hilly areas, and artificial soil is often sprayed onto them to promote ecological rehabilitation. The artificial soil properties are very important for effective management of the slopes. This paper uses fractal and moment methods to characterize soil particle size distribution (PSD) and aggregates composition. The fractal dimension (D) showed linear relationships between clay, silt, and sand contents, with coefficients of determination from 0.843 to 0.875, suggesting that using of D to evaluate the PSD of artificial soils is reasonable. The bias (CS) and peak convex (CE) coefficients showed significant correlations with structure failure rate, moisture content, and total porosity, which validated the moment method to quantitatively describe soil structure. Railway slope (RS) soil has lower organic carbon and soil moisture, and higher pH than natural slope soil. Overall, RS exhibited poor soil structure and physicochemical properties, increasing the risk of soil erosion. Hence, more effective management measures should be adopted to promote the restoration of cut slopes. PMID:26883986

Urbanization Effects on the Vertical Distribution of Soil Microbial Communities and Soil C Storage across Edge-to-Interior Urban Forest Gradients

NASA Astrophysics Data System (ADS)

Rosier, C. L.; Van Stan, J. T., II; Trammell, T. L.

2017-12-01

Urbanization alters environmental conditions such as temperature, moisture, carbon (C) and nitrogen (N) deposition affecting critical soil processes (e.g., C storage). Urban soils experience elevated N deposition (e.g., transportation, industry) and decreased soil moisture via urban heat island that can subsequently alter soil microbial community structure and activity. However, there is a critical gap in understanding how increased temperatures and pollutant deposition influences soil microbial community structure and soil C/N cycling in urban forests. Furthermore, canopy structural differences between individual tree species is a potentially important mechanism facilitating the deposition of pollutants to the soil. The overarching goal of this study is to investigate the influence of urbanization and tree species structural differences on the bacterial and fungal community and C and N content of soils experiencing a gradient of urbanization pressures (i.e., forest edge to interior; 150-m). Soil cores (1-m depth) were collected near the stem (< 0.5 meter) of two tree species with contrasting canopy and bark structure (Fagus grandifolia, vs. Liriodendron tulipifera), and evaluated for soil microbial structure via metagenomic analysis and soil C/N content. We hypothesize that soil moisture constraints coupled with increases in recalcitrant C will decrease gram negative bacteria (i.e., dependent on labile C) while increasing saprophytic fungal community abundance (i.e., specialist consuming recalcitrant C) within both surface and subsurface soils experiencing the greatest urban pressure (i.e., forest edge). We further expect trees located on the edge of forest fragments will maintain greater surface soil (< 20 cm) C concentrations due to decreased soil moisture constraining microbial activity (e.g., slower decay), and increased capture of recalcitrant C stocks from industrial/vehicle emission sources (e.g., black C). Our initial results support our hypotheses that urbanization alters soil microbial community composition via reduced soil moisture and carbon storage potential via deposition gradients. Further analyses will answer important questions regarding how individual tree species alters urban soil C storage, N retention, and microbial dynamics.

Soil structural quality assessment for soil protection regulation

NASA Astrophysics Data System (ADS)

Johannes, Alice; Boivin, Pascal

2017-04-01

Soil quality assessment is rapidly developing worldwide, though mostly focused on the monitoring of arable land and soil fertility. Soil protection regulations assess soil quality differently, focusing on priority pollutants and threshold values. The soil physical properties are weakly considered, due to lack of consensus and experimental difficulties faced with characterization. Non-disputable, easy to perform and inexpensive methods should be available for environmental regulation to be applied, which is unfortunately not the case. As a consequence, quantitative soil physical protection regulation is not applied, and inexpensive soil physical quality indicators for arable soil management are not available. Overcoming these limitations was the objective of a research project funded by the Swiss federal office for environment (FOEN). The main results and the perspectives of application are given in this presentation. A first step of the research was to characterize soils in a good structural state (reference soils) under different land use. The structural quality was assessed with field expertise and Visual Evaluation of the Soil Structure (VESS), and the physical properties were assessed with Shrinkage analysis. The relationships between the physical properties and the soil constituents were linear and highly determined. They represent the reference properties of the corresponding soils. In a second step, the properties of physically degraded soils were analysed and compared to the reference properties. This allowed defining the most discriminant parameters departing the different structure qualities and their threshold limits. Equivalent properties corresponding to these parameters but inexpensive and easy to determine were defined and tested. More than 90% of the samples were correctly classed with this method, which meets, therefore, the requirements for practical application in regulation. Moreover, result-oriented agri-environmental schemes for soil quality are now proposed to farmers based on these indicators.

The effect of total carbon on microscopic soil properties and implications for crop production

USDA-ARS?s Scientific Manuscript database

Soil structure is a dynamic property affected by physical, chemical, and microbiological processes. Addition of organic matter to soils and the use of different management practices have been reported to impact soil structure and crop production. Moderation in soil temperature and increases in mic...

Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra.

PubMed

Kim, Hye Min; Lee, Min Jin; Jung, Ji Young; Hwang, Chung Yeon; Kim, Mincheol; Ro, Hee-Myong; Chun, Jongsik; Lee, Yoo Kyung

2016-11-01

The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.

[Soil microbial community structure in Picea asperata plantations with different ages in subalpine of western Sichuan, Southwest China.

PubMed

Luo, Da; Liu, Shun; Shi, Zuo Min; Feng, Qiu Hong; Liu, Qian Li; Zhang, Li; Huang, Quan; He, Jian She

2017-02-01

The effects of four Picea asperata plantations with different ages (50-, 38-, 27- and 20-year-old), in subalpine of western Sichuan, on the characteristics of soil microbial diversity and microbial community structure were studied by the method of phospholipid fatty acid (PLFA) profiles. The results showed that, with the increase of age, the contents of soil organic carbon and total nitrogen gradually improved, while Shannon's diversity index and Pielou's evenness index of soil microorganisms increased at first and then decreased. The amounts of microbial total PLFAs, bacterial PLFAs, fungal PLFAs, actinobacterial PLFAs, and arbuscular mycorrhizal fungal (AMF) PLFAs in soils consistently increased with increasing age. The principal component analysis (PCA) indicated that the soil microbial communities in different plantations were structurally distinct from each other. The first principal component (PC1) and the second principal component (PC2) together accounted for 66.8% of total variation of the soil microbial community structure. The redundancy analysis (RDA) of soil microbial community structure and environmental factors showed that soil organic carbon, total nitrogen, total potassium, and fine root mass were the key determinants influencing the microbial community structure. Our study suggested that, with the extension of artificialafforestation time, the soil fertility and microbial biomass were enhanced, and the restoration processes of forest ecosystem were stable.

Effects of drought on forest soil structure and hydrological soil functions

NASA Astrophysics Data System (ADS)

Gimbel, K.; Puhlmann, H.; Weiler, M.

2012-04-01

Climate change is predicted to severely affect precipitation patterns across central Europe. Soil structure is closely linked to the activity of soil microbiota and plant roots, which modify flow pathways along roots, organic matter and water repellence of soils. Through shrinkage and fracturing of soil aggregates, soil structure is also responding to changing climate (in particular drought) conditions. We investigate the possible effects on biogeochemical and hydropedological processes in response to predicted future reduced precipitation, and the interaction of these processes with the biodiversity of the forest understorey and soil biota. The hypotheses of this study are: (i) drought causes a change in soil structure, which affects hydrological soil functions (water infiltration, uptake and redistribution); (ii) changes in rooting patterns and microbial community composition, in response to drought, influence the hydrological soil functions. To test our hypotheses, we built adaptive roofing systems on nine sites in Germany, which allow a flexible reduction of precipitation in order to achieve the long-term minimum precipitation of a site. Here we present first measurements of our repeated measuring/sampling campaign, which will be conducted over a period of three years. The aim of our experiments is to analyze soil pore architecture and related flow and transport behaviour with dye tracer sprinkling experiments, soil column experiments with stable isotope (deuterium, oxygen-18) enriched water, computed tomography at soil monoliths (~70 l) and multi-step outflow experiments with 100 ml soil cores. Finally, we sketch our idea how to relate the observed temporal changes of soil structure and hydrological soil functions to the observed dynamics of hydrometeorological site conditions, soil moisture and desiccation as well as changes in rooting patterns, herb layer and soil microbiotic communities. The results of this study may help to assess future behavior of the plant-soil-water-microbiology-system and may help to adjust models to predict future response to different precipitation patterns as well as help coping with existing and future emerging challenges in forest management.

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

PubMed Central

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils. PMID:28611747

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

PubMed

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

Correlation between soil physicochemical properties and vegetation parameters in secondary tropical forest in Sabal, Sarawak, Malaysia

NASA Astrophysics Data System (ADS)

Karyati, K.; Ipor, I. B.; Jusoh, I.; Wasli, M. E.

2018-04-01

The tree growth is influenced by soil morphological and physicochemical properties in the site. The purpose of this study was to describe correlation between soil properties under various stage secondary forests and vegetation parameters, such as floristic structure parameters and floristic diversity indices. The vegetation surveys were conducted in 5, 10, and 20 years old at secondary tropical forests in Sarawak, Malaysia. Nine sub plots sized 20 m × 20 m were established within each study site. The Pearson analysis showed that soil physicochemical properties were significantly correlated to floristic structure parameters and floristic diversity indices. The result of PCA clarified the correlation among most important soil properties, floristic structure parameters, and floristic diversity indices. The PC1 represented cation retention capacity and soil texture which were little affected by the fallow age and its also were correlated by floristic structure and diversity. The PC2 was linked to the levels of soil acidity. This property reflected the remnant effects of ash addition and fallow duration, and the significant correlation were showed among pH (H2O), floristic structure and diversity. The PC3 represented the soil compactness. The soil hardness could be influenced by fallow period and it was also correlated by floristic structure.

Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

PubMed

Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

2015-09-01

Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.

Importance of inoculum properties on the structure and growth of bacterial communities during Recolonisation of humus soil with different pH.

PubMed

Pettersson, Marie; Bååth, Erland

2013-08-01

The relationship between community structure and growth and pH tolerance of a soil bacterial community was studied after liming in a reciprocal inoculum study. An unlimed (UL) humus soil with a pH of 4.0 was fumigated with chloroform for 4 h, after which < 1 % of the initial bacterial activity remained. Half of the fumigated soil was experimentally limed (EL) to a pH of 7.6. Both the UL and the EL soil were then reciprocally inoculated with UL soil or field limed (FL) soil with a pH of 6.2. The FL soil was from a 15-year-old experiment. The structural changes were measured on both bacteria in soil and on bacteria able to grow on agar plates using phospholipids fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analysis. The developing community pH tolerance and bacterial growth were also monitored over time using thymidine incorporation. The inoculum source had a significant impact on both growth and pH tolerance of the bacterial community in the EL soil. These differences between the EL soil inoculated with UL soil and FL soil were correlated to structural changes, as evidenced by both PLFA and DGGE analyses on the soil. Similar correlations were seen to the fraction of the community growing on agar plates. There were, however, no differences between the soil bacterial communities in the unlimed soils with different inocula. This study showed the connection between the development of function (growth), community properties (pH tolerance) and the structure of the bacterial community. It also highlighted the importance of both the initial properties of the community and the selection pressure after environmental changes in shaping the resulting microbial community.

Soil fungi colony growth and community dynamics

NASA Astrophysics Data System (ADS)

Falconer, Ruth E.; Kravchenko, Alexandra; Otten, Wilfred

2010-05-01

Fungi are a major player in soil functioning, they contribute to soil structure formation and shaping of plant communities through their role in nutrient cycling, pathogenesis and symbiosis. Theoretical approaches which have emerged over the years and improved considerably our understanding of above ground plant communities are still lacking below ground. A theoretical framework is needed, such that links soil physics, fungal biology and mathematical biology in order to understand fungal community dynamics and diversity in undisturbed soils. Such a framework is essential if we are to understand how environmental change or soil manipulation impacts biodiversity. Different land use and management practices significantly affect soil environmental characteristics crucial for fungal communities by contributing different quantities and qualities of biomass inputs, generating different levels of soil disturbance, influencing soil temperature and moisture regimes, and affecting structure and geometry of soil pore space. Differences in pore structures generated by long-term differences in land use and management are reflected in notable changes in soil physical and hydraulic properties, including soil porosity, hydraulic conductivity and water retention (Brye and Pirani, 2005). Changes in numbers, shapes, and distributions of soil macropores have been often observed (e.g., Pachepsky et al., 1996; Giménez et al., 1997; Udawatta et al., 2008). However, specific implications of these differences in pore structure and geometries for ability of pathogenic as well as non-pathogenic fungi to colonize soil have not yet been addressed. Recent advances in computed tomography and microscopy facilitate detailed examination of the inner pore structures of undisturbed soil samples as well as visualization of fungal mycelia. Such tools together with modelling generate a new level of understanding of the mechanisms governing fungal behaviour at microscopic scales, and for the first time allow us to examine species interactions in a 3D soil environment.

Effects of Rainfall-Induced Topsoil Structure Changes on Root-Zone Moisture Regime during the Dry Period

NASA Astrophysics Data System (ADS)

Wang, Feng; Chen, Jiazhou; Lin, Lirong

2018-01-01

Rainfall erosion and subsequent intermittent drought are serious barriers for agricultural production in the subtropical red soil region of China. Although it is widely recognized that rainfall-induced soil structure degradation reduced soil water storage and water-holding capacity, the effects of variation of the rainfall-induced topsoil structure on the subsequent soil water regime during the dry period is still rarely considered. The objective of this study was to ascertain the way of rainfall-induced topsoil structure changes on the subsequent soil water regime during the dry period. In a three-year-long experiment, six practices (CK, only crop; SM, straw mulching; PAM, polyacrylamide surface application; B, contour Bahia-grass strip; SPAM, straw mulching and polyacrylamide surface application; and BPAM, contour Bahia-grass strip and polyacrylamide surface application) were conducted at an 8° farmland with planting summer maize resulting in different topsoil structure and root-zone moisture, to establish and reveal the quantitatively relationship between the factors of topsoil structure and soil drought. Rainfall erosion significantly increased the soil crust coverage, and decreased the WSA 0.25, 0-30 mm soil porosity and mean pore size. There was no significant difference during the raining stage of root-zone water storage between CK and other practices. An index of soil drought intensity ( I) and degree ( D) was established using soil water loss rate and soil drought severity. The larger value of I means a higher rate of water loss. The larger value of D means more severe drought. During the dry period, I and D were significantly higher in CK than in other practices. I and D had significantly positively correlation with the crust size and crust coverage, and negatively with WSA 0.25, 15-30 mm soil porosity and mean pore size. Among of soil structure factors, the soil porosity had the largest effect on I and D. The rainfall-induced topsoil structure changes greatly deteriorated the root-zone regime during the dry period mainly due to significant increasing soil water loss but little improving the raining stage of soil water storage. Straw mulching had greater effects than other practices in alleviating rainfall-induced erosion and intermittent drought, and could be a better strategy applied for this region.

Forest canopy structural controls over throughfall affect soil microbial community structure in an epiphyte-laden maritime oak stand

NASA Astrophysics Data System (ADS)

Van Stan, J. T., II; Rosier, C. L.; Schrom, J. O.; Wu, T.; Reichard, J. S.; Kan, J.

2014-12-01

Identifying spatiotemporal influences on soil microbial community (SMC) structure is critical to understanding of patterns in nutrient cycling and related ecological services. Since forest canopy structure alters the spatiotemporal patterning of precipitation water and solute supplies to soils (via the "throughfall" mechanism), is it possible changes in SMC structure variability could arise from modifications in canopy elements? Our study investigates this question by monitoring throughfall water and dissolved ion supply to soils beneath a continuum of canopy structure: from a large gap (0% cover) to heavy Tillandsia usneoides L. (Spanish moss) canopy (>90% cover). Throughfall water supply diminished with increasing canopy cover, yet increased washoff/leaching of Na+, Cl-, PO43-, and SO42- from the canopy to the soils (p < 0.01). Presence of T. usneoides diminished throughfall NO3-, but enhanced NH4+, concentrations supplied to subcanopy soils. The mineral soil horizon (0-10 cm) from canopy gaps, bare canopy, and T. usneoides-laden canopy significantly differed (p < 0.05) in soil chemistry parameters (pH, Ca2+, Mg2+, CEC). PCR-DGGE banding patterns beneath similar canopy covers (experiencing similar throughfall dynamics) also produced high similarities per ANalyses Of SIMilarity (ANO-SIM), and clustered together when analyzed by Nonmetric Multidimensional Scaling (NMDS). Correlation analysis of DGGE banding patterns, throughfall dynamics, and soil chemistry yielded significant correlations (p < 0.05) between fungal communities and soil chemical properties significantly differing between canopy cover types (pH: r2 = 0.50; H+ %-base saturation: r2 = 0.48; Ca2+ %-base saturation: r2 = 0.43). Bacterial community structure correlated with throughfall NO3-, NH4+, and Ca2+ concentrations (r2 = 0.37, p = 0.16). These results suggest that modifications of forest canopy structures are capable of affecting mineral-soil horizon SMC structure via the throughfall mechanism when canopies' biomass distribution is highly heterogeneous.

76 FR 70057 - National Oil and Hazardous Substance Pollution Contingency Plan; National Priorities List...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

... surface soils, subsurface soils, structures and groundwater within the boundaries of these parcels. In... soils, subsurface soils, structures and groundwater within the boundaries of the non-ETA part of PIN 05... additional contaminated groundwater and soil within the Site. On November 25, 2005 EPA partially deleted the...

Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

PubMed

Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

2017-08-16

Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

Effects of different regulatory methods on improvement of greenhouse saline soils, tomato quality, and yield.

PubMed

Maomao, Hou; Xiaohou, Shao; Yaming, Zhai

2014-01-01

To identify effective regulatory methods scheduling with the compromise between the soil desalination and the improvement of tomato quality and yield, a 3-year field experiment was conducted to evaluate and compare the effect of straw mulching and soil structure conditioner and water-retaining agent on greenhouse saline soils, tomato quality, and yield. A higher salt removing rate of 80.72% in plough layer with straw mulching was obtained based on the observation of salt mass fraction in 0 ~ 20 cm soil layer before and after the experiment. Salts were also found to move gradually to the deeper soil layer with time. Straw mulching enhanced the content of soil organic matter significantly and was conductive to reserve soil available N, P, and K, while available P and K in soils of plough layer with soil structure conditioner decreased obviously; thus a greater usage of P fertilizer and K fertilizer was needed when applying soil structure conditioner. Considering the evaluation indexes including tomato quality, yield, and desalination effects of different regulatory methods, straw mulching was recommended as the main regulatory method to improve greenhouse saline soils in south China. Soil structure conditioner was the suboptimal method, which could be applied in concert with straw mulching.

Pore-scale water dynamics during drying and the impacts of structure and surface wettability

NASA Astrophysics Data System (ADS)

Cruz, Brian C.; Furrer, Jessica M.; Guo, Yi-Syuan; Dougherty, Daniel; Hinestroza, Hector F.; Hernandez, Jhoan S.; Gage, Daniel J.; Cho, Yong Ku; Shor, Leslie M.

2017-07-01

Plants and microbes secrete mucilage into soil during dry conditions, which can alter soil structure and increase contact angle. Structured soils exhibit a broad pore size distribution with many small and many large pores, and strong capillary forces in narrow pores can retain moisture in soil aggregates. Meanwhile, contact angle determines the water repellency of soils, which can result in suppressed evaporation rates. Although they are often studied independently, both structure and contact angle influence water movement, distribution, and retention in soils. Here drying experiments were conducted using soil micromodels patterned to emulate different aggregation states of a sandy loam soil. Micromodels were treated to exhibit contact angles representative of those in bulk soil (8.4° ± 1.9°) and the rhizosphere (65° ± 9.2°). Drying was simulated using a lattice Boltzmann single-component, multiphase model. In our experiments, micromodels with higher contact angle surfaces took 4 times longer to completely dry versus micromodels with lower contact angle surfaces. Microstructure influenced drying rate as a function of saturation and controlled the spatial distribution of moisture within micromodels. Lattice Boltzmann simulations accurately predicted pore-scale moisture retention patterns within micromodels with different structures and contact angles.

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand.

PubMed

Truu, Marika; Ostonen, Ivika; Preem, Jens-Konrad; Lõhmus, Krista; Nõlvak, Hiie; Ligi, Teele; Rosenvald, Katrin; Parts, Kaarin; Kupper, Priit; Truu, Jaak

2017-01-01

Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch ( Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N 2 O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity.

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand

PubMed Central

Truu, Marika; Ostonen, Ivika; Preem, Jens-Konrad; Lõhmus, Krista; Nõlvak, Hiie; Ligi, Teele; Rosenvald, Katrin; Parts, Kaarin; Kupper, Priit; Truu, Jaak

2017-01-01

Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch (Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N2O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity. PMID:28421053

Visual soil evaluation - future research requirements

NASA Astrophysics Data System (ADS)

Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Ball, Bruce; Holden, Nick

2017-04-01

A review of Visual Soil Evaluation (VSE) techniques (Emmet-Booth et al., 2016) highlighted their established utility for soil quality assessment, though some limitations were identified; (1) The examination of aggregate size, visible intra-porosity and shape forms a key assessment criterion in almost all methods, thus limiting evaluation to structural form. The addition of criteria that holistically examine structure may be desirable. For example, structural stability can be indicated using dispersion tests or examining soil surface crusting, while the assessment of soil colour may indirectly indicate soil organic matter content, a contributor to stability. Organic matter assessment may also indicate structural resilience, along with rooting, earthworm numbers or shrinkage cracking. (2) Soil texture may influence results or impeded method deployment. Modification of procedures to account for extreme texture variation is desirable. For example, evidence of compaction in sandy or single grain soils greatly differs to that in clayey soils. Some procedures incorporate separate classification systems or adjust deployment based on texture. (3) Research into impacts of soil moisture content on VSE evaluation criteria is required. Criteria such as rupture resistance and shape may be affected by moisture content. It is generally recommended that methods are deployed on moist soils and quantification of influences of moisture variation on results is necessary. (4) Robust sampling strategies for method deployment are required. Dealing with spatial variation differs between methods, but where methods can be deployed over large areas, clear instruction on sampling is required. Additionally, as emphasis has been placed on the agricultural production of soil, so the ability of VSE for exploring structural quality in terms of carbon storage, water purification and biodiversity support also requires research. References Emmet-Booth, J.P., Forristal. P.D., Fenton, O., Ball, B.C. & Holden, N.M. 2016. A review of visual soil evaluation techniques for soil structure. Soil Use and Management, 32, 623-634.

Assessing agricultural management effects on structure related soil hydraulic properties by tension infiltrometry

NASA Astrophysics Data System (ADS)

Bodner, G.; Loiskandl, W.; Kaul, H.-P.

2009-04-01

Soil structure is a dynamic property subject to numerous natural and human influences. It is recognized as fundamental for sustainable functioning of soil. Therefore knowledge of management impacts on the sensitive structural states of soil is decisive in order to avoid soil degradation. The stabilization of the soil's (macro)pore system and eventually the improvement of its infiltrability are essential to avoid runoff and soil erosion, particularly in view of an increasing probability of intense rainfall events. However structure-related soil properties generally have a high natural spatiotemporal variability that interacts with the potential influence of agricultural land use. This complicates a clear determination of management vs. environmental effects and requires adequate measurement methods, allowing a sufficient spatiotemporal resolution to estimate the impact of the targeted management factors within the natural dynamics of soil structure. A common method to assess structure-related soil hydraulic properties is tension infiltrometry. A major advantage of tension infiltrometer measurements is that no or only minimum soil disturbance is necessary and several structure-controlled water transmission properties can readily be derived. The method is more time- and cost-efficient compared to laboratory measurements of soil hydraulic properties, thus enabling more replications. Furthermore in situ measurements of hydraulic properties generally allow a more accurate reproduction of field soil water dynamics. The present study analyses the impact of two common agricultural management options on structure related hydraulic properties based on tension infiltrometer measurements. Its focus is the identification of the role of management within the natural spatiotemporal variability, particularly in respect to seasonal temporal dynamics. Two management approaches are analysed, (i) cover cropping as a "plant-based" agro-environmental measure, and (ii) tillage with different intensities including conventional tillage with a mouldboard plough, reduced tillage with a chisel plough and no-tillage. The results showed that the plant-based management measure of cover cropping had only minor influence on near-saturated hydraulic conductivity (kh) and flow weighted mean pore radius (λm). Substantial over-winter changes were found with a significant increase in kh and a reduction in the pore radius. A spatial trend in soil texture along the cover cropped slope resulted in a higher kh at lower pressure heads at the summit with higher fractions of coarse particles, while kh tended to be highest at the toeslope towards saturation. Cover crop management accounted for a maximum of 9.7% of the total variability in kh, with a decreasing impact towards the unsaturated range. A substantial difference to bare soil in the cover cropped treatments could be identified in relation to a stabilization of macro-pores over winter. The different tillage treatments had a substantial impact on near-saturated kh and pore radius. Although conventional tillage showed the highest values in kh and λm, settling of the soil after the ploughing event tended to reduce differences over time compared to the other tillage methods. The long-term no-tillage (10 years) however had the lowest values of kh at all measurement dates. The high contents of silt and fine sand probably resulted in soil densification that was not counterbalanced sufficiently by biological structure forming agents. The study could show that soil structure related hydraulic properties are subject to a substantial seasonal variability. A comprehensive assessment of agricultural measures such as tillage or cover cropping requires an estimate of these temporal dynamics and their interaction with the management strategies. Particularly for plant-based management measures such as cover cropping, which represent a less intense intervention in the structural states of the soil compared to tillage, this was evident, as the main mechanism revealed for this measure was structure stabilization over time. While spatial variability is mostly controlled in designed experiments, the role of temporal variability is often underestimated. From our study we concluded that (i) a proper understanding of processes involved in management effects on soil structure must take into consideration the dynamic nature of the respective soil properties, (ii) experimental planning for studies regarding management impacts on soil structure should allow an estimation of temporal variability, and (iii) for this purpose tension infiltrometry provides an efficient measurement tool to assess structure related soil hydraulic properties.

Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH.

PubMed

Zhang, Yuting; Shen, Hong; He, Xinhua; Thomas, Ben W; Lupwayi, Newton Z; Hao, Xiying; Thomas, Matthew C; Shi, Xiaojun

2017-01-01

Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007-2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1.0%); the least abundant phyla were Verrucomicrobia (0.7%), Armatimonadetes (0.6%), candidate division WS3 (0.4%) and Fibrobacteres (0.3%). In addition, Cyanobacteria and candidate division TM7 were more abundant in acidic soil, whereas Gemmatimonadetes, Nitrospirae and candidate division WS3 were more abundant in alkaline soil. We conclude that after 7-years of fertilization, soil bacterial diversity and community structure were shaped more by changes in soil pH rather than the direct effect of nutrient addition.

Throughfall-mediated alterations to soil microbial community structure in a forest plot of homogenous soil texture, litter, and plant species composition

NASA Astrophysics Data System (ADS)

Van Stan, John; Rosier, Carl; Moore, Leslie; Gay, Trent; Reichard, James; Wu, Tiehang; Kan, Jinjun

2015-04-01

Identifying spatiotemporal influences on soil microbial community (SMC) structure is critical to our understanding of patterns in biogeochemical cycling and related ecological services (e.g., plant community structure, water quality, response to environmental change). Since forest canopy structure alters the spatiotemporal patterning of precipitation water and solute supplies to soils (via "throughfall"), is it possible that changes in SMC structure could arise from modifications in canopy elements? Our study investigates this question by monitoring throughfall water and dissolved ion supply to soils beneath a continuum of canopy structure: from large gaps (0% cover), to bare Quercus virginiana Mill. (southern live oak) canopy (~50-70%), to heavy Tillandsia usneoides L. (Spanish moss) canopy (>90% cover). Throughfall water supply diminished with increasing canopy cover, yet increased washoff/leaching of Na+, Cl-, PO43-, and SO42- from the canopy to the soils. Presence of T. usneoides diminished throughfall NO3-, but enhanced NH4+, concentrations supplied to subcanopy soils. The mineral soil horizon (0-10 cm) sampled in triplicate from locations receiving throughfall water and solutes from canopy gaps, bare canopy, and T. usneoides-laden canopy significantly differed in soil chemistry parameters (pH, Ca2+, Mg2+, CEC). Polymerase Chain Reaction-Denaturant Gradient Gel Electrophoresis (PCR-DGGE) banding patterns beneath similar canopy covers (experiencing similar throughfall dynamics) also produced high similarities per ANalyses Of SIMilarity (ANO-SIM), and clustered together when analyzed by Nonmetric Multidimensional Scaling (NMDS). These results suggest that modifications of forest canopy structures are capable of affecting mineral-soil horizon SMC structure via throughfall when canopies' biomass distribution is highly heterogeneous. As SMC structure, in many instances, relates to functional diversity, we suggest that future research seek to identify functional diversity shifts (e.g., nitrogen transformation) in response to canopy structural alterations of throughfall water/solute concentration

Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

PubMed

Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

2014-08-01

The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

Assessing the variation in bund structure design and its impact on soil physical properties and hydrology in Koga catchment, Highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Lakew, Walle; Baartman, Jantiene; Fleskens, Luuk; Selassie, Yihenew; Ritsema, Coen

2017-04-01

Prolonged soil drying and severe moisture stress during the dry season, and soil saturation and erosion during the short rainy season are critical problems in the Ethiopian highlands. Large-scale implementation of bund structures has been used as soil and water management (SWM) strategy to fight these problems and establish a sustainable land management (SLM) system. However, many SWM practices are implemented with design flaws or without proper design and maintenance, and do not match conservation requirements. The quality of implementation and effects of bund structures on soil physical properties is not yet documented. Therefore, in this study, field investigations and laboratory analysis were carried out to evaluate the variation in bund structure design and its impact on soil-water retention, bulk density, porosity and soil depth. Results show that the dimensions and stability of bund structures, and consequently, the impacts of bunds varied widely. The widths and heights of bunds, and slope gradients were significantly correlated with infiltration rate and available soil-water content. Water holding capacity was 24% higher compared to that on untreated farms. Bunds with larger dimensions of top width (>85 cm) and height (>75 cm) showed 17 and 18% higher water holding capacity compared to fields with bunds having lower dimensions. In addition, results exhibited that the porosity and soil depth were significantly affected by the dimensions of bund structures and increased with increasing widths and heights of bunds. A 14.2% increase in porosity; a 41.2% increase in infiltration rate; and a 17.5% decrease in bulk density was found in soils of treated farms compared to those of untreated farm plots. Differences in particle size distribution and soil erodibility among widths of the bunds were low. It can be concluded that bund structure design varied substantially throughout the study area, which had impacted soil-water storage and soil physical properties. Bund structure design should be adapted to local biophysical settings at catchment level to enhance on- and offsite impacts.

Assessment the effect of homogenized soil on soil hydraulic properties and soil water transport

NASA Astrophysics Data System (ADS)

Mohawesh, O.; Janssen, M.; Maaitah, O.; Lennartz, B.

2017-09-01

Soil hydraulic properties play a crucial role in simulating water flow and contaminant transport. Soil hydraulic properties are commonly measured using homogenized soil samples. However, soil structure has a significant effect on the soil ability to retain and to conduct water, particularly in aggregated soils. In order to determine the effect of soil homogenization on soil hydraulic properties and soil water transport, undisturbed soil samples were carefully collected. Five different soil structures were identified: Angular-blocky, Crumble, Angular-blocky (different soil texture), Granular, and subangular-blocky. The soil hydraulic properties were determined for undisturbed and homogenized soil samples for each soil structure. The soil hydraulic properties were used to model soil water transport using HYDRUS-1D.The homogenized soil samples showed a significant increase in wide pores (wCP) and a decrease in narrow pores (nCP). The wCP increased by 95.6, 141.2, 391.6, 3.9, 261.3%, and nCP decreased by 69.5, 10.5, 33.8, 72.7, and 39.3% for homogenized soil samples compared to undisturbed soil samples. The soil water retention curves exhibited a significant decrease in water holding capacity for homogenized soil samples compared with the undisturbed soil samples. The homogenized soil samples showed also a decrease in soil hydraulic conductivity. The simulated results showed that water movement and distribution were affected by soil homogenizing. Moreover, soil homogenizing affected soil hydraulic properties and soil water transport. However, field studies are being needed to find the effect of these differences on water, chemical, and pollutant transport under several scenarios.

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

PubMed

You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

2014-03-01

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.

Radon entry into basements: Approach, experimental structures, and instrumentation of the small structures research project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fisk, W.J.; Modera, M.P.; Sextro, R.G.

1992-02-01

We describe the experimental approach, structures, and instrumentation of a research project on radon generation and transport in soil and entry into basements. The overall approach is to construct small precisely-fabricated basements in areas of different geology and climate, to control the pressures and ventilation rates in the structures, and to monitor radon concentrations and other relevant parameters over a period of one year or more. Two nearly air-tight structures have been constructed at the first site. The floor of each structure contains adjustable-width slots that serve as the only significant pathway for advective entry of radon. A layer ofmore » gravel underlays the floor of one structure; otherwise they are identical. The structures are instrumented for continuous or periodic monitoring of soil, structural, and meteorological parameters that affect radon entry. The pressure difference that drives advective radon entry can be maintained constant or varied over time. Soil gas and radon entry rates and associated parameters, such as soil gas pressures and radon concentrations, have been monitored for a range of steady-state and time-varying pressure differences between the interior of the structure and the soil. Examples of the experimentally-measured pressure and permeability fields in the soil around a structure are presented and discussed.« less

Evolution of Pedostructure Parameters Under Tillage Practices

USDA-ARS?s Scientific Manuscript database

The pedostructure (PS) concept is a physically-based method of soil characterization that defines a soil based on its structure and the relationship between structure and soil water behavior. There are 15 unique pedostructure parameters that define the macropore and micropore soil water behavior fo...

Response of soil biota to vineyard interrow soil cultivation can be altered by the surrounding landscape

NASA Astrophysics Data System (ADS)

Zaller, Johann; Buchholz, Jacob; Querner, Pascal; Paredes, Daniel; Kratschmer, Sophie; Schwantzer, Martina; Winter, Silvia; Strauss, Peter; Bauer, Thomas; Burel, Françoise; Guernion, Muriel; Scimia, Jennifer; Nicolai, Annegret; Cluzeau, Daniel

2017-04-01

Ecosystem services provided by viticultural landscapes result from interactions between management intensity, soil properties, organisms inhabiting these landscapes, and the diversity and structure of the surrounding landscape. However, there is actually very little known to what extent these different factors influence the abundance and diversity of various soil biota. In this study we examined (i) to what extent different soil management intensities of interrows affect the activity and diversity of soil biota (earthworms, Collembola, litter decomposition), (ii) the role of soil properties in influencing these effects and (iii) whether the surrounding landscape structure is altering these interactions. We collected data in 16 vineyards in Austria embedded in landscapes with varying structure (i.e. from structurally simple to complex) and assessed earthworms (hand sorting), Collembola (pitfall trapping and soil coring), litter decomposition (tea bag method). Additionally, soil physical (water infiltration, aggregate stability, porosity, bulk density, soil texture) and chemical (pH, soil carbon content, cation exchange capacity, potassium, phosphorus) parameters were assessed. The landscape surrounding our vineyards within a radius of 750 m was assessed by field mapping using a geographical information system. Results showed that different soil biota/processes are differently affected by soil cultivation intensity and soil properties. Parameters describing the surrounding landscape interacted more with the responses of Collembola to soil cultivation than with earthworms or litter decomposition. These investigations are part of the transdisciplinary BiodivERsA project VineDivers (www.vinedivers.eu) and will ultimately lead into management recommendations for various stakeholders.

[Soil microbial community structure of monoculture and mixed plantation stands of native tree species in south subtropical China].

PubMed

Luo, Da; Shi, Zuo-Min; Tang, Jing-Chao; Liu, Shi-Rong; Lu, Li-Hua

2014-09-01

The effects of three plantation stands, Erythrophleumf ordii (EF), Pinus massoniana (PM), and their mixed plantation (MP), on soil microbial biomass and microbial community structure in south subtropical China were studied by the method of phospholipid fatty acids (PLFAs) analysis. The results showed that the amounts of microbial total PLFAs and PLFAs of each microbial group in these three plantation stand soils were significantly higher in dry season than in rainy season. In dry season, the amounts of microbial total PLFAs, bacteria PLFAs, fungi PLFAs, and actinomycetes PLFAs were the highest in the PM soil, moderate in the MP soil, and the lowest in the EF soil. But in rainy season, the amounts of microbial total PLFAs, bacteria PLFAs, fungi PLFAs, and arbuscular mycorrhizal fungi (AMF) PLFAs in the EF soil were higher than in the MP soil, and were significantly higher than in the PM soil. Principal component analysis (PCA) indicated that the variations in soil microbial community structure composition were affected by both plantation types and seasons. Redundancy analysis (RDA) of soil microbial community structure and environmental factors showed that soil temperature and moisture, pH, total nitrogen content, and ammonium nitrogen content had significant correlations with PLFA signatures. In addition, the ratio of fungi PLFAs to bacteria PLFAs in the MP soil was the highest among the three stand soils within the whole year, indicating that mixed plantation stands could facilitate the stability of the soil ecosystem.

Model structures amplify uncertainty in predicted soil carbon responses to climate change.

PubMed

Shi, Zheng; Crowell, Sean; Luo, Yiqi; Moore, Berrien

2018-06-04

Large model uncertainty in projected future soil carbon (C) dynamics has been well documented. However, our understanding of the sources of this uncertainty is limited. Here we quantify the uncertainties arising from model parameters, structures and their interactions, and how those uncertainties propagate through different models to projections of future soil carbon stocks. Both the vertically resolved model and the microbial explicit model project much greater uncertainties to climate change than the conventional soil C model, with both positive and negative C-climate feedbacks, whereas the conventional model consistently predicts positive soil C-climate feedback. Our findings suggest that diverse model structures are necessary to increase confidence in soil C projection. However, the larger uncertainty in the complex models also suggests that we need to strike a balance between model complexity and the need to include diverse model structures in order to forecast soil C dynamics with high confidence and low uncertainty.

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

PubMed Central

Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

2014-01-01

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

SITE AMPLIFICATION OF EARTHQUAKE GROUND MOTION.

USGS Publications Warehouse

Hays, Walter W.

1986-01-01

When analyzing the patterns of damage in an earthquake, physical parameters of the total earthquake-site-structure system are correlated with the damage. Soil-structure interaction, the cause of damage in many earthquakes, involves the frequency-dependent response of both the soil-rock column and the structure. The response of the soil-rock column (called site amplification) is controversial because soil has strain-dependent properties that affect the way the soil column filters the input body and surface seismic waves, modifying the amplitude and phase spectra and the duration of the surface ground motion.

Future Carbon Dynamics of the Northern Rockies Ecoregion due to Climate Impacts and Fire Effects

NASA Astrophysics Data System (ADS)

Weller, U.; Lang, B.; Rabot, E.; Stössel, B.; Urbanski, L.; Vogel, H. J.; Wiesmeier, M.; Wollschlaeger, U.

2016-12-01

The impact of agricultural management on soil functions is manifold and severe. It has both positive and adverse influence. Our goal is to develop model tools quantifying the agricultural impact on soil functions based on a mechanistic understanding of soil processes to support farmers and decision makers. The modeling approach is based on defining relevant soil components, i.e. soil matrix, macropores, organisms, roots and organic matter. They interact and form the soil's macroscopic properties and functions including water and gas dynamics, and biochemical cycles. Based on existing literature information we derive functional interaction processes and combine them in a network of dynamic soil components. In agricultural soils, a major issue is linked to changes in soil structure and their influence on water dynamics. Compaction processes are well studied in literature, but for the resilience due to root growth and activity of soil organisms the information is scarcer. We implement structural dynamics into soil water and gas simulations using a lumped model that is both coarse enough to allow extensive model runs while still preserving some important, yet rarely modeled phenomenons like preferential flow, hysteretic and dynamic behavior. For simulating water dynamics, at each depth, the model assumes water at different binding energies depending on soil structure, i.e. the pore size distribution. Non-equilibrium is postulated, meaning that free water may occur even if the soil is not fully saturated. All energy levels are interconnected allowing water to move, both within a spatial node, and between neighboring nodes (adding gravity). Structure dynamics alters the capacity of this water compartments, and the conductance of its connections. Connections are switched on and off depending on whether their sources contain water or their targets have free capacity. This leads to piecewise linear system behavior that allows fast calculation for extended time steps. Based on this concept, the dynamics of soil structure can be directly linked to soil water dynamics as a main driver for other soil processes. Further steps will include integration of temperature and solute leaching as well as defining the feedback of the water regime on the structure forming processes.

Build your own soil: exploring microfluidics to create microbial habitat structures

PubMed Central

Aleklett, Kristin; Kiers, E Toby; Ohlsson, Pelle; Shimizu, Thomas S; Caldas, Victor EA; Hammer, Edith C

2018-01-01

Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats. PMID:29135971

Chemical evaluation of soil organic matter structure in diverse cropping systems

USDA-ARS?s Scientific Manuscript database

Soil organic matter (SOM) improves soil structure, nutrient and water retention, and biodiversity while reducing susceptibility to soil erosion. SOM also represents an important pool of C that can be increased to help mitigate global climate change. Our understanding of how agricultural management ...

Improvements of the Profil Cultural Method for a better Low-tech Field Assessment of Soil Structure under no-till

NASA Astrophysics Data System (ADS)

Roger-Estrade, Jean; Boizard, Hubert; Peigné, Josephine; Sasal, Maria Carolina; Guimaraes, Rachel; Piron, Denis; Tomis, Vincent; Vian, Jean-François; Cadoux, Stephane; Ralisch, Ricardo; Filho, Tavares; Heddadj, Djilali; de Battista, Juan; Duparque, Annie

2016-04-01

In France, agronomists have studied the effects of cropping systems on soil structure, using a field method based on a visual description of soil structure. The "profil cultural" method (Manichon and Gautronneau, 1987) has been designed to perform a field diagnostic of the effects of tillage and compaction on soil structure dynamics. This method is of great use to agronomists improving crop management for a better preservation of soil structure. However, this method was developed and mainly used in conventional tillage systems, with ploughing. As several forms of reduced, minimum and no tillage systems are expanding in many parts of the world, it is necessary to re-evaluate the ability of this method to describe and interpret soil macrostructure in unploughed situations. In unploughed fields, soil structure dynamics of untilled layers is mainly driven by compaction and regeneration by natural agents (climatic conditions, root growth and macrofauna) and it is of major importance to evaluate the importance of these natural processes on soil structure regeneration. These concerns have led us to adapt the standard method and to propose amendments based on a series of field observations and experimental work in different situations of cropping systems, soil types and climatic conditions. We improved the description of crack type and we introduced an index of biological activity, based on the visual examination of clods. To test the improved method, a comparison with the reference method was carried out and the ability of the "profil cultural" method to make a diagnosis was tested on five experiments in France, Brazil and Argentina. Using the improved method, the impact of cropping systems on soil functioning was better assessed when natural processes were integrated into the description.

Beech cupules as keystone structures for soil fauna.

PubMed

Melguizo-Ruiz, Nereida; Jiménez-Navarro, Gerardo; Moya-Laraño, Jordi

2016-01-01

Facilitative or positive interactions are ubiquitous in nature and play a fundamental role in the configuration of ecological communities. In particular, habitat modification and niche construction, in which one organism locally modifies abiotic conditions and favours other organisms by buffering the effects of adverse environmental factors, are among the most relevant facilitative interactions. In line with this, 'keystone structures', which provide resources, refuge, or advantageous services decisive for other species, may allow the coexistence of various species and thus considerably contribute to diversity maintenance. Beech cupules are woody husks harbouring beech fruits that remain in the forest soil for relatively long periods of time. In this study, we explored the potential role of these cupules in the distribution and maintenance of the soil fauna inhabiting the leaf litter layer. We experimentally manipulated cupule availability and soil moisture in the field to determine if such structures are limiting and can provide moist shelter to soil animals during drought periods, contributing to minimize desiccation risks. We measured invertebrate abundances inside relative to outside the cupules, total abundances in the leaf litter and animal body sizes, in both dry and wet experimental plots. We found that these structures are preferentially used by the most abundant groups of smaller soil animals-springtails, mites and enchytraeids-during droughts. Moreover, beech cupules can be limiting, as an increase in use was found with higher cupule densities, and are important resources for many small soil invertebrates, driving the spatial structure of the soil community and promoting higher densities in the leaf litter, probably through an increase in habitat heterogeneity. We propose that fruit woody structures should be considered 'keystone structures' that contribute to soil community maintenance. Therefore, beech trees may indirectly facilitate soil fauna activities through their decaying fruit husks, hence acting as ecosystem engineers.

Modelling soil-water dynamics in the rootzone of structured and water-repellent soils

NASA Astrophysics Data System (ADS)

Brown, Hamish; Carrick, Sam; Müller, Karin; Thomas, Steve; Sharp, Joanna; Cichota, Rogerio; Holzworth, Dean; Clothier, Brent

2018-04-01

In modelling the hydrology of Earth's critical zone, there are two major challenges. The first is to understand and model the processes of infiltration, runoff, redistribution and root-water uptake in structured soils that exhibit preferential flows through macropore networks. The other challenge is to parametrise and model the impact of ephemeral hydrophobicity of water-repellent soils. Here we have developed a soil-water model, which is based on physical principles, yet possesses simple functionality to enable easier parameterisation, so as to predict soil-water dynamics in structured soils displaying time-varying degrees of hydrophobicity. Our model, WEIRDO (Water Evapotranspiration Infiltration Redistribution Drainage runOff), has been developed in the APSIM Next Generation platform (Agricultural Production Systems sIMulation). The model operates on an hourly time-step. The repository for this open-source code is https://github.com/APSIMInitiative/ApsimX. We have carried out sensitivity tests to show how WEIRDO predicts infiltration, drainage, redistribution, transpiration and soil-water evaporation for three distinctly different soil textures displaying differing hydraulic properties. These three soils were drawn from the UNSODA (Unsaturated SOil hydraulic Database) soils database of the United States Department of Agriculture (USDA). We show how preferential flow process and hydrophobicity determine the spatio-temporal pattern of soil-water dynamics. Finally, we have validated WEIRDO by comparing its predictions against three years of soil-water content measurements made under an irrigated alfalfa (Medicago sativa L.) trial. The results provide validation of the model's ability to simulate soil-water dynamics in structured soils.

The mechanics and energetics of soil bioturbation by earthworms and plant roots - Impacts on soil structure generation and maintenance

NASA Astrophysics Data System (ADS)

Or, Dani; Ruiz, Siul; Schymanski, Stanlislaus

2015-04-01

Soil structure is the delicate arrangement of solids and voids that facilitate numerous hydrological and ecological soil functions ranging from water infiltration and retention to gaseous exchange and mechanical anchoring of plant roots. Many anthropogenic activities affect soil structure, e.g. via tillage and compaction, and by promotion or suppression of biological activity and soil carbon pools. Soil biological activity is critical to the generation and maintenance of favorable soil structure, primarily through bioturbation by earthworms and root proliferation. The study aims to quantify the mechanisms, rates, and energetics associated with soil bioturbation, using a new biomechanical model to estimate stresses required to penetrate and expand a cylindrical cavity in a soil under different hydration and mechanical conditions. The stresses and soil displacement involved are placed in their ecological context (typical sizes, population densities, burrowing rates and behavior) enabling estimation of mechanical energy requirements and impacts on soil organic carbon pool (in the case of earthworms). We consider steady state plastic cavity expansion to determine burrowing pressures of earthworms and plant roots, akin to models of cone penetration representing initial burrowing into soil volumes. Results show that with increasing water content the strain energy decreases and suggest trade-offs between cavity expansion pressures and energy investment for different root and earthworm geometries and soil hydration. The study provides a quantitative framework for estimating energy costs of bioturbation in terms of soil organic carbon or the mechanical costs of soil exploration by plant roots as well as mechanical and hydration limits to such activities.

Study on soil-pile-structure-TMD interaction system by shaking table model test

NASA Astrophysics Data System (ADS)

Lou, Menglin; Wang, Wenjian

2004-06-01

The success of the tuned mass damper (TMD) in reducing wind-induced structural vibrations has been well established. However, from most of the recent numerical studies, it appears that for a structure situated on very soft soil, soil-structure interaction (SSI) could render a damper on the structure totally ineffective. In order to experimentally verify the SSI effect on the seismic performance of TMD, a series of shaking table model tests have been conducted and the results are presented in this paper. It has been shown that the TMD is not as effective in controlling the seismic responses of structures built on soft soil sites due to the SSI effect. Some test results also show that a TMD device might have a negative impact if the SSI effect is neglected and the structure is built on a soft soil site. For structures constructed on a soil foundation, this research verifies that the SSI effect must be carefully understood before a TMD control system is designed to determine if the control is necessary and if the SSI effect must be considered when choosing the optimal parameters of the TMD device.

75 FR 16202 - Office of New Reactors; Interim Staff Guidance on Ensuring Hazard-Consistent Seismic Input for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-31

... Staff Guidance on Ensuring Hazard-Consistent Seismic Input for Site Response and Soil Structure...-Consistent Seismic Input for Site Response and Soil Structure Interaction Analyses,'' (Agencywide Documents... Soil Structure Interaction Analyses,'' (ADAMS Accession No. ML092230455) to solicit public and industry...

The vertical geography of urban soils and its convergence across cities

EPA Science Inventory

The theoretical patterns for vertical soil structure (e.g., A-B-C ordering of horizons) are a basis for research methods and our understanding of ecosystem structure and function in general. A general understanding of how urban soils differ from non-urban soils vertically is need...

Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment

DOE PAGES

Bond-Lamberty, Benjamin; Bolton, Harvey; Fansler, Sarah J.; ...

2016-03-02

The effects of climate change on soil organic matter—its structure, microbial community, carbon storage, and respiration response—remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampledmore » the original 1994 soil transplants and controls, measuring CO 2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5 °C monthly maximum air temperature, +50 mm yr -1precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. Lastly, these results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.« less

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

PubMed Central

2012-01-01

Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree. PMID:22873209

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment.

PubMed

Bond-Lamberty, Ben; Bolton, Harvey; Fansler, Sarah; Heredia-Langner, Alejandro; Liu, Chongxuan; McCue, Lee Ann; Smith, Jeffrey; Bailey, Vanessa

2016-01-01

The effects of climate change on soil organic matter-its structure, microbial community, carbon storage, and respiration response-remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampled the original 1994 soil transplants and controls, measuring CO2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5°C monthly maximum air temperature, +50 mm yr-1 precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. These results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.

Evaluating the importance of characterizing soil structure and horizons in parameterizing a hydrologic process model

USGS Publications Warehouse

Mirus, Benjamin B.

2015-01-01

Incorporating the influence of soil structure and horizons into parameterizations of distributed surface water/groundwater models remains a challenge. Often, only a single soil unit is employed, and soil-hydraulic properties are assigned based on textural classification, without evaluating the potential impact of these simplifications. This study uses a distributed physics-based model to assess the influence of soil horizons and structure on effective parameterization. This paper tests the viability of two established and widely used hydrogeologic methods for simulating runoff and variably saturated flow through layered soils: (1) accounting for vertical heterogeneity by combining hydrostratigraphic units with contrasting hydraulic properties into homogeneous, anisotropic units and (2) use of established pedotransfer functions based on soil texture alone to estimate water retention and conductivity, without accounting for the influence of pedon structures and hysteresis. The viability of this latter method for capturing the seasonal transition from runoff-dominated to evapotranspiration-dominated regimes is also tested here. For cases tested here, event-based simulations using simplified vertical heterogeneity did not capture the state-dependent anisotropy and complex combinations of runoff generation mechanisms resulting from permeability contrasts in layered hillslopes with complex topography. Continuous simulations using pedotransfer functions that do not account for the influence of soil structure and hysteresis generally over-predicted runoff, leading to propagation of substantial water balance errors. Analysis suggests that identifying a dominant hydropedological unit provides the most acceptable simplification of subsurface layering and that modified pedotransfer functions with steeper soil-water retention curves might adequately capture the influence of soil structure and hysteresis on hydrologic response in headwater catchments.

Vibration control of a cluster of buildings through the Vibrating Barrier

NASA Astrophysics Data System (ADS)

Tombari, A.; Garcia Espinosa, M.; Alexander, N. A.; Cacciola, P.

2018-02-01

A novel device, called Vibrating Barrier (ViBa), that aims to reduce the vibrations of adjacent structures subjected to ground motion waves has been recently proposed. The ViBa is a structure buried in the soil and detached from surrounding buildings that is able to absorb a significant portion of the dynamic energy arising from the ground motion. The working principle exploits the dynamic interaction among vibrating structures due to the propagation of waves through the soil, namely the structure-soil-structure interaction. In this paper the efficiency of the ViBa is investigated to control the vibrations of a cluster of buildings. To this aim, a discrete model of structures-site interaction involving multiple buildings and the ViBa is developed where the effects of the soil on the structures, i.e. the soil-structure interaction (SSI), the structure-soil-structure interaction (SSSI) as well as the ViBa-soil-structures interaction are taken into account by means of linear elastic springs. Closed-form solutions are derived to design the ViBa in the case of harmonic excitation from the analysis of the discrete model. Advanced finite element numerical simulations are performed in order to assess the efficiency of the ViBa for protecting more than a single building. Parametric studies are also conducted to identify beneficial/adverse effects in the use of the proposed vibration control strategy to protect cluster of buildings. Finally, experimental shake table tests are performed to a prototype of a cluster of two buildings protected by the ViBa device for validating the proposed numerical models.

Changes in bacterial diversity associated with bioremediation of used lubricating oil in tropical soils.

PubMed

Meeboon, Naruemon; Leewis, Mary-Cathrine; Kaewsuwan, Sireewan; Maneerat, Suppasil; Leigh, Mary Beth

2017-08-01

Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C). We further explored the relationship between bacterial community structure, physiochemical soil parameters, and ULO composition in three ULO-contaminated soils. Results indicated that the three investigated soils had different community structures, which may be a result of the different ULO characteristics and physiochemical soil parameters of each site. Soil C had the highest ULO concentration and also the greatest diversity and richness of bacteria, which may be a result of higher nutrient retention, organic matter and cation exchange capacity, as well as freshness of oil compared to the other soils. In soils A and B, Proteobacteria (esp. Gammaproteobacteria) dominated the bacterial community, and in soil C, Actinobacteria and Firmicutes dominated. The genus Enterobacter, a member of the class Gammaproteobacteria, is known to include ULO-degraders, and this genus was the only one found in all three soils, suggesting that it could play a key role in the in situ degradation of ULO-contaminated tropical Thai soils. This study provides insights into our understanding of soil microbial richness, diversity, composition, and structure in tropical ULO-contaminated soils, and may be useful for the development of strategies to improve bioremediation.

Microbial community structure and activity in a Colorado Rocky Mountain forest soil scarred by slash pile burning

Treesearch

Aida E. Jimenez Esquilin; Mary E. Stromberger; William J. Massman; John M. Frank; Wayne D. Shepperd

2007-01-01

Tree thinning and harvesting produces large amounts of slash material which are typically disposed of by burning, often resulting in severe soil heating. We measured soil chemical properties and microbial community structure and function over time to determine effects of slash pile burning in a ponderosa pine forest soil. Real time data were collected for soil...

Humic Substances in Organic Wastes and their Effects on Amended Soils

NASA Astrophysics Data System (ADS)

Senesi, N.; Ciavatta, C.; Plaza, C.

2009-04-01

Soil humic substances (HS) are universally recognized to play a major role in a wide number of agronomic and environmental processes. For example, soil HS are able to bind mineral particles together, thus promoting a good soil structure, constitute an important source of nutrients for plants and microorganisms, contribute largely to the acid-base buffering capacity of soils, and exert a marked control on the biological availability, physico-chemical behavior, and environmental fate of toxic metal ions and xenobiotics. For these reasons, the knowledge of the short- and long-term effects of organic amendments on the status, quality, and reactivity of indigenous soil HS is of paramount importance. The objective of this presentation is to provide an overview of the chemical and physico-chemical data available in the literature for the evaluation of the effects of organic wastes of various origin and nature used as soil amendments on the composition, structure, and chemical reactivity of native soil HS. In general, HS-like components of organic wastes are typically characterized by a relatively larger presence of aliphatic, amide, and polysaccharide structures, simple structural components of wide molecular heterogeneity, smaller contents of oxygen, acidic functional groups, and organic free radicals, and smaller degrees of aromatic ring polycondensation, polymerization, and humification than native soil HS. Further, with respect to native soil HS, HS-like fractions from organic wastes generally exhibit smaller binding capacities and affinities for metal ions and organic xenobiotics. Appropriate treatment processes of raw organic wastes able to produce environmentally safe and agronomically efficient soil amendments, such as composting, yield HS-like fractions characterized by chemical and physico-chemical features that approach those of native soil HS. In general, aliphatic, polysaccharide, and lignin structures and S- and N-containing groups of the HS-like fractions of organic wastes can be partially incorporated into native soil HS determining modifications at various extents of their composition, structure, and chemistry. The changes occurred in amended soil HS are more evident when untreated organic materials are used. However, with increasing time after land application, the effects observed become less and less apparent with a clear trend to approach the molecular properties typical of native soil HS.

Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil.

PubMed

Val-Moraes, Silvana Pompeia; de Macedo, Helena Suleiman; Kishi, Luciano Takeshi; Pereira, Rodrigo Matheus; Navarrete, Acacio Aparecido; Mendes, Lucas William; de Figueiredo, Eduardo Barretto; La Scala, Newton; Tsai, Siu Mui; de Macedo Lemos, Eliana Gertrudes; Alves, Lúcia Maria Carareto

2016-12-01

Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.

Soil cover of gas-bearing areas

NASA Astrophysics Data System (ADS)

Mozharova, N. V.

2010-08-01

Natural soils with disturbed functioning parameters compared to the background soils with conservative technogenic-pedogenic features were distinguished on vast areas above the artificial underground gas storages in the zones of spreading and predominant impact of hydrocarbon gases. The disturbance of the functioning parameters is related to the increase in the methane concentration, the bacterial oxidation intensity and destruction, and the complex microbiological and physicochemical synthesis of iron oxides. The technogenic-pedogenic features include neoformations of bacteriomorphic microdispersed iron oxides. The impurity components consist of elements typical for biogenic structures. New soil layers, horizons, specific anthropogenically modified soils, and soil-like structures were formed on small areas in the industrial zones of underground gas storages due to the mechanical disturbance, the deposition of drilling sludge, and the chemical contamination. Among the soils, postlithogenic formations were identified—chemotechnosols (soddy-podzolic soils and chernozems), as well as synlithogenic ones: strato-chemotechnosols and stratochemoembryozems. The soil-like bodies included postlithogenic soil-like structures (chemotechnozems) and synlithogenic ones (strato-chemotechnozems). A substantive approach was used for the soil diagnostics. The morphological and magnetic profiles and the physical, chemical, and physicochemical properties of the soils were analyzed. The micromorphological composition of the soil magnetic fraction was used as a magnetic label.

[Effects of different fertilization treatments on soil humic acid structure characteristics].

PubMed

Zhao, Nan; Lü, Yi-Zhong

2012-07-01

The present article used soil humic acid as research object to study effects on the structure characteristics of soil humic acid under the condition of applying cake fertilizer, green manure, straw fertilizer with the same contents of nitrogen and phosphorus. It used element analysis, micro infrared, and solid 13C-NMR for structure analysis, the results indicated that: The chemical composition and structure characteristics of humic acids were similar, but they also had many obvious differences. (1) The atomic ratios of H/C, O/C, and C/N were all different for the humic acids, the soil humic acid of cake fertilizer processing had the highest contents of H and N, green manure processing of soil humic acid contained the highest content of O, while straw fertilizer processing of soil humic acid contained highest content of C. (2) Infrared analysis displayed that the three soil humic acids contained protein Cake fertilizer processing of soil humic acid contained the most amino compounds, green manure processing of soil humic acid contained the maximum contents of hydroxyl and aliphatic hydrocarbon, while straw fertilizer processing of soil humic acid contained the highest contents of alcohol and phenol. (3) Solid 13C-NMR data indicated that cake fertilizer processing of soil humic acid contained the most carboxyl carbon, green manure processing of soil humic acid contained the highest contents of alkyl carbon and carbonyl carbon, while straw fertilizer processing of soil humic acids had the most alkoxy carbon and aromatic carbon

Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

PubMed

Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

2014-03-01

Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p < 0.001). Amplicons of AOA from the Nitrososphaera cluster dominated all four ecosystem soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bacterial diversity of soil aggregates of different sizes in various land use conditions

NASA Astrophysics Data System (ADS)

Ivanova, Ekaterina; Azida, Thakahova; Olga, Kutovaya

2014-05-01

The patterns of soil microbiome structure may be a universal and very sensitive indicator of soil quality (soil "health") used for optimization and biologization of agricultural systems. The understanding of how microbial diversity influenses, and is influenced by, the environment can only be attained by analyses at scales relevant to those at which processes influencing microbial diversity actually operate. The basic structural and functional unit of the soil is a soil aggregate, which is actually a microcosm of the associative co-existing groups of microorganisms that form characteristic ecological food chains. It is known that many important microbial processes occur in spatially segregated microenvironments in soil leading to a microscale biogeography. The Metagenomic library of typical chernozem in conditions of different land use systems was created. Total genomic DNA was extracted from 0.5 g of the frozen soil after mechanical destruction. Sample preparation and sequencing was performed on a GS Junior ("Roche»", Switzerland) according to manufacturer's recommendations, using the universal primers to the variable regions V4 gene 16S - rRNA - F515 (GTGCCAGCMGCCGCGGTAA) and R806 (GGACT-ACVSGGGTATCTAAT). It is shown that the system of land use is a stronger determinant of the taxonomic composition of the soil microbial community, rather than the size of the structural units. In soil samples from different land use systems the presence of accessory components was revealed. They may be used as indicators of processes of soil recovery, soil degradation or soil exhaustion processes occuring in the agroecosystems. The comparative analysis of microbial communities of chernozem aggregates investigated demonstrates the statistically valuable differences in the amount of bacterial phyla and Archean domain content as well as the species richness in aggregates of various size fractions. The occurrence of specific components in the taxonomic structure of micro-and macro-aggregates may indicate the presence of a certain size fraction in the structure of the investigated soil. The study of soils' metagenome is promising for the development of both soil microbiology, and for the soil processes trends in soils of anthropogenic origin.

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-10-01

Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were better explained using both soil physicochemical test values and bacterial community structure data than using soil tests alone. Pursuing a better understanding of bacterial community composition and how it is affected by farming practices is a promising avenue for increasing our ability to predict the impact of management practices on important soil functions. Copyright © 2016. Published by Elsevier B.V.

Nitrogen-mediated effects of elevated CO2 on intra-aggregate soil pore structure

USDA-ARS?s Scientific Manuscript database

While previous elevated atmospheric CO2 research has addressed changes in belowground processes, its effects on soil structure remain virtually undescribed. This study examined the long-term effects of elevated CO2 and N fertilization on soil structural changes in a bahiagrass pasture grown on a san...

Correlation of soil microbes and soil micro-environment under long-term safflower (Carthamus tinctorius L.) plantation in China.

PubMed

Lu, Shuang; Quan, Wang; Wang, Shao-Ming; Liu, Hong-Ling; Tan, Yong; Zeng, Guang-Ping; Zhang, Xia

2013-04-01

Microbial community structure and ecological functions are influenced by interactions between above and belowground biota. There is an urgent need for intensive monitoring of microbes feedback of soil micro-ecosystem for setting up a good agricultural practice. Recent researches have revealed that many soils characteristic can effect microbial community structure. In the present study factors affecting microbial community structure and soil in Carthamus tinctorius plantations in arid agricultural ecosystem of northern Xinjiang, China were identified. The result of the study revealed that soil type was the key factor in safflower yield; Unscientific field management resulted high fertility level (bacteria dominant) of soil to turn to low fertility level (fungi dominant), and Detruded Canonical Correspondence Analysis (DCCA) showed that soil water content, organic matter, available N, P and K were the dominant factors affecting distribution of microbial community. Soil water content showed a significant positive correlation with soil microbes quantity (P < 0.01), while others showed a significant quantity correlation with soil microbe quantity (P < 0.05).

Dullgren extraction of soil mites (Acarina): Effect of refrigeration time on extraction efficiency

Treesearch

Michelle B. Lakly; D.A. Crossley

2000-01-01

Soil microarthropods constitute one of the most species rich communities in . forest ecosystems (Crossley & Blair, 1991). The effects of soil fauna in these systems on decomposition rates, nutrient regeneration and soil structure have been well documented; however, dependable estimates of population size and community structure largely depend upon adequate sampling...

Universal Spatial Correlation Functions for Describing and Reconstructing Soil Microstructure

PubMed Central

Skvortsova, Elena B.; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity. PMID:26010779

Universal spatial correlation functions for describing and reconstructing soil microstructure.

PubMed

Karsanina, Marina V; Gerke, Kirill M; Skvortsova, Elena B; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity.

Impact of rhizobial inoculation on Acacia senegal (L.) Willd. growth in greenhouse and soil functioning in relation to seed provenance and soil origin.

PubMed

Bakhoum, Niokhor; Ndoye, Fatou; Kane, Aboubacry; Assigbetse, Komi; Fall, Dioumacor; Sylla, Samba Ndao; Noba, Kandioura; Diouf, Diégane

2012-07-01

Rhizobial inoculation has a positive impact on plants growth; however, there is little information about its effect on soil microbial communities and their activity in the rhizosphere. It was therefore necessary to test the effect of inoculation of Acacia senegal (L.) Willd. seedlings with selected rhizobia on plant growth, structure and diversity of soil bacterial communities and soil functioning in relation to plant provenance and soil origin. In order to carry out this experiment, three A. senegal seeds provenance from Kenya, Niger, and Senegal were inoculated with selected rhizobial strains. They have been further grown during 4 months in greenhouse conditions in two non-disinfected soils, Dahra and Goudiry coming respectively from arid and semi-arid areas. The principal component analysis (ACP) showed an inoculation effect on plant growth, rhizospheric bacterial diversity and soil functioning. However, the performances of the rhizobial strains varied in relation to the seed provenance and the soil origin. The selected rhizobial strains, the A. senegal provenance and the soil origin have modified the structure and the diversity of soil bacterial communities as measured by principal component analysis/denaturing gradient gel electrophoresis analyses. It is interesting to note that bacterial communities of Dahra soil were highly structured according to A. senegal provenance, whereas they were structured in relation to rhizobial inoculation in Goudiry soil. Besides, the impact of inoculation on soil microbial activities measured by fluorescein diacetate analyses varied in relation to plant provenance and soil origin. Nevertheless, total microbial activity was about two times higher in Goudiry, arid soil than in Dahra, semi-arid soil. Our results suggest that the rhizobial inoculation is a suitable tool for improving plants growth and soil fertility. Yet, the impact is dependent on inoculants, plant provenance and soil origin. It will, therefore, be crucial to identify the appropriate rhizobial strains and plant provenance or species in relation to the soil type.

Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs.

PubMed

Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin

2011-10-01

Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Geotechnical centrifuge use at University of Cambridge Geotechnical Centre, August-September 1991

NASA Astrophysics Data System (ADS)

Gilbert, Paul A.

1992-01-01

A geotechnical centrifuge applies elevated acceleration to small-scale soil models to simulate body forces and stress levels characteristic of full-size soil structures. Since the constitutive behavior of soil is stress level development, the centrifuge offers considerable advantage in studying soil structures using models. Several experiments were observed and described in relative detail, including experiments in soil dynamics and liquefaction study, an experiment investigation leaning towers on soft foundations, and an experiment investigating migration of hot pollutants through soils.

[Effects of biochar application on the abundance and structure of ammonia-oxidizer communities in coal-mining area.

PubMed

Liu, Yuan; Zhu, Ji Rong; Wu, Yu Chen; Shu, Liang Zuo

2017-10-01

As a new type of soil amendment, biochar can effectively improve soil fertility, structure and soil nitrogen transformation. We studied the effects of biochar application on soil properties, abundance and community structure of ammonia oxidizer in coal-mining area. The results showed that the biochar application significantly increased contents of soil NH4+-N, total nitrogen, available phosphorus and potassium. Compared with the control, no change in the abundance of ammonia-oxidizing archaea (AOA) was found under biochar treatment, but there was a significant increase in the abundance of ammonia-oxidizing bacteria (AOB). The analysis of T-RFLP profiles showed that biochar significantly increased the diversity indexes of AOA and AOB, and altered the community structure of both AOA and AOB. Improved soil nutrients as well as increased abundance and diversity of ammonia-oxidizing community to some extent indicated the potential of biochar application in reclamation of coal-mining area soil.

3D soil structure characterization of Biological Soil Crusts from Alpine Tarfala Valley

NASA Astrophysics Data System (ADS)

Mele, Giacomo; Gargiulo, Laura; Zucconi, Laura; D'Acqui, Luigi; Ventura, Stefano

2017-04-01

Cyanobacteria filaments, microfungal hyphae, lichen rhizinae and anchoring rhizoids of bryophytes all together contribute to induce formation of structure in the thin soil layer beneath the Biological Soil Crusts (BSCs). Quantitative assessment of the soil structure beneath the BSCs is primarily hindered by the fragile nature of the crusts. Therefore, the role of BSCs in affecting such soil physical property has been rarely addressed using direct measurements. In this work we applied non-destructive X-ray microtomography imaging on five different samples of BSCs collected in the Alpine Tarfala Valley (northern Sweden), which have already been characterized in terms of fungal biodiversity in a previous work. We obtained images of the 3D spatial organization of the soil underneath the BSCs and characterized its structure by applying procedures of image analysis allowing to determine pore size distribution, pore connectivity and aggregate size distribution. Results has then been correlated with the different fungal assemblages of the samples.

Soil microbial community successional patterns during forest ecosystem restoration.

PubMed

Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

2011-09-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

PubMed Central

Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

2011-01-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890

Green roof soil system affected by soil structural changes: A project initiation

NASA Astrophysics Data System (ADS)

Jelínková, Vladimíra; Dohnal, Michal; Šácha, Jan; Šebestová, Jana; Sněhota, Michal

2014-05-01

Anthropogenic soil systems and structures such as green roofs, permeable or grassed pavements comprise appreciable part of the urban watersheds and are considered to be beneficial regarding to numerous aspects (e.g. carbon dioxide cycle, microclimate, reducing solar absorbance and storm water). Expected performance of these systems is significantly affected by water and heat regimes that are primarily defined by technology and materials used for system construction, local climate condition, amount of precipitation, the orientation and type of the vegetation cover. The benefits and potencies of anthropogenic soil systems could be considerably threatened in case when exposed to structural changes of thin top soil layer in time. Extensive green roof together with experimental green roof segment was established and advanced automated monitoring system of micrometeorological variables was set-up at the experimental site of University Centre for Energy Efficient Buildings as an interdisciplinary research facility of the Czech Technical University in Prague. The key objectives of the project are (i) to characterize hydraulic and thermal properties of soil substrate studied, (ii) to establish seasonal dynamics of water and heat in selected soil systems from continuous monitoring of relevant variables, (iii) to detect structural changes with the use of X-ray Computed Tomography, (iv) to identify with the help of numerical modeling and acquired datasets how water and heat dynamics in anthropogenic soil systems are affected by soil structural changes. Achievements of the objectives will advance understanding of the anthropogenic soil systems behavior in conurbations with the temperate climate.

[Analysis of soil humus and components after 26 years' fertilization by infrared spectroscopy method].

PubMed

Zhang, Yu-Lan; Sun, Cai-Xia; Chen, Zhen-Hua; Li, Dong-Po; Liu, Xing-Bin; Chen, Li-Jun; Wu, Zhi-Jie; Du, Jian-Xiong

2010-05-01

The infrared spectrum was used to discuss structure change of soil humus and components of chemical groups in soil humic acids (HA) and fulvic acids (FA) isolated from soils in different fertilization treatment after 26 year's fertilization. The result indicated that using the infrared spectroscopy method for the determination of humus, humus fractions (HA and FA) and their structure is feasible. Fertilization affected the structure and content of soil humus and aromatization degree. After 26 years' fertilization, the infrared spectrum shapes with different treatments are similar, but the characteristic peak intensity is obviously different, which reflects the effects of different fertilization treatments on the structure and amounts of soil humus or functional groups. Compared with no fertilization, little molecule saccharides decreased and aryl-groups increased under application of inorganic fertilizer or combined application of organic and chemical fertilizer. The effect was greater in Treatment NPK and M+NPK than in Treatment M1 N and M2 N. Organic and NPK fertilizer increased the development of soil and increased soil quality to a certain extent. Results showed that organic fertilization increased aromatization degree of soil humus and humus fractions distinctly. The authors could estimate soil humus evolvement of different fertilization with infrared spectroscopy.

Soil compaction: Evaluation of stress transmission and resulting soil structure

NASA Astrophysics Data System (ADS)

Naveed, Muhammad; Schjønning, Per; Keller, Thomas; Lamande, Mathieu

2016-04-01

Accurate estimation of stress transmission and resultant deformation in soil profiles is a prerequisite for the development of predictive models and decision support tools for preventing soil compaction. Numerous studies have been carried out on the effects of soil compaction, whilst relatively few studies have focused on the cause (mode of stress transmission in the soil). We have coupled both cause and effects together in the present study by carrying out partially confined compression tests on (1) wet aggregates, (2) air dry aggregates, and (3) intact soils to quantify stress transmission and compaction-resulted soil structure at the same time. Stress transmission was quantified using both X-ray CT and Tactilus sensor mat, and soil-pore structure was quantified using X-ray CT. Our results imply that stress transmission through soil highly depends on the magnitude of applied load and aggregate strength. As soon as the applied load is lower than the aggregate strength, the mode of stress transmission is discrete as stresses were mainly transmitted through chain of aggregates. With increasing applied load soil aggregates start deforming that transformed heterogeneous soil into homogenous, as a result stress transmission mode was shifted from discrete towards more like a continuum. Continuum-like stress transmission mode was better simulated with Boussinesq (1885) model based on theory of elasticity compared to discrete. The soil-pore structure was greatly affected by increasing applied stresses. Total porosity was reduced 5-16% and macroporosity 50-85% at 620 kPa applied stress for the intact soils. Similarly, significant changes in the morphological indices of the macropore space were also observed with increasing applied stresses.

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

PubMed

Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

2016-02-01

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Nonlinear Time Domain Seismic Soil-Structure Interaction (SSI) Deep Soil Site Methodology Development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spears, Robert Edward; Coleman, Justin Leigh

Currently the Department of Energy (DOE) and the nuclear industry perform seismic soil-structure interaction (SSI) analysis using equivalent linear numerical analysis tools. For lower levels of ground motion, these tools should produce reasonable in-structure response values for evaluation of existing and new facilities. For larger levels of ground motion these tools likely overestimate the in-structure response (and therefore structural demand) since they do not consider geometric nonlinearities (such as gaping and sliding between the soil and structure) and are limited in the ability to model nonlinear soil behavior. The current equivalent linear SSI (SASSI) analysis approach either joins the soilmore » and structure together in both tension and compression or releases the soil from the structure for both tension and compression. It also makes linear approximations for material nonlinearities and generalizes energy absorption with viscous damping. This produces the potential for inaccurately establishing where the structural concerns exist and/or inaccurately establishing the amplitude of the in-structure responses. Seismic hazard curves at nuclear facilities have continued to increase over the years as more information has been developed on seismic sources (i.e. faults), additional information gathered on seismic events, and additional research performed to determine local site effects. Seismic hazard curves are used to develop design basis earthquakes (DBE) that are used to evaluate nuclear facility response. As the seismic hazard curves increase, the input ground motions (DBE’s) used to numerically evaluation nuclear facility response increase causing larger in-structure response. As ground motions increase so does the importance of including nonlinear effects in numerical SSI models. To include material nonlinearity in the soil and geometric nonlinearity using contact (gaping and sliding) it is necessary to develop a nonlinear time domain methodology. This methodology will be known as, NonLinear Soil-Structure Interaction (NLSSI). In general NLSSI analysis should provide a more accurate representation of the seismic demands on nuclear facilities their systems and components. INL, in collaboration with a Nuclear Power Plant Vender (NPP-V), will develop a generic Nuclear Power Plant (NPP) structural design to be used in development of the methodology and for comparison with SASSI. This generic NPP design has been evaluated for the INL soil site because of the ease of access and quality of the site specific data. It is now being evaluated for a second site at Vogtle which is located approximately 15 miles East-Northeast of Waynesboro, Georgia and adjacent to Savanna River. The Vogtle site consists of many soil layers spanning down to a depth of 1058 feet. The reason that two soil sites are chosen is to demonstrate the methodology across multiple soil sites. The project will drive the models (soil and structure) using successively increasing acceleration time histories with amplitudes. The models will be run in time domain codes such as ABAQUS, LS-DYNA, and/or ESSI and compared with the same models run in SASSI. The project is focused on developing and documenting a method for performing time domain, non-linear seismic soil structure interaction (SSI) analysis. Development of this method will provide the Department of Energy (DOE) and industry with another tool to perform seismic SSI analysis.« less

A radiosity-based model to compute the radiation transfer of soil surface

NASA Astrophysics Data System (ADS)

Zhao, Feng; Li, Yuguang

2011-11-01

A good understanding of interactions of electromagnetic radiation with soil surface is important for a further improvement of remote sensing methods. In this paper, a radiosity-based analytical model for soil Directional Reflectance Factor's (DRF) distributions was developed and evaluated. The model was specifically dedicated to the study of radiation transfer for the soil surface under tillage practices. The soil was abstracted as two dimensional U-shaped or V-shaped geometric structures with periodic macroscopic variations. The roughness of the simulated surfaces was expressed as a ratio of the height to the width for the U and V-shaped structures. The assumption was made that the shadowing of soil surface, simulated by U or V-shaped grooves, has a greater influence on the soil reflectance distribution than the scattering properties of basic soil particles of silt and clay. Another assumption was that the soil is a perfectly diffuse reflector at a microscopic level, which is a prerequisite for the application of the radiosity method. This radiosity-based analytical model was evaluated by a forward Monte Carlo ray-tracing model under the same structural scenes and identical spectral parameters. The statistics of these two models' BRF fitting results for several soil structures under the same conditions showed the good agreements. By using the model, the physical mechanism of the soil bidirectional reflectance pattern was revealed.

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

NASA Astrophysics Data System (ADS)

Jha, Neha; Saggar, Surinder; Giltrap, Donna; Tillman, Russ; Deslippe, Julie

2017-09-01

Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N2O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N2O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N2O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N2O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N2O emissions through denitrification across a wide range of soil types.

Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling.

PubMed

Berthrong, Sean T; Buckley, Daniel H; Drinkwater, Laurie E

2013-07-01

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.

Soil physical land degradation processes

NASA Astrophysics Data System (ADS)

Horn, Rainer

2017-04-01

According to the European Soil Framework Directive (2006) soil compaction is besides water and wind erosion one of the main physical reasons and threats of soil degradation. It is estimated, that 32% of the subsoils in Europe are highly degraded and 18% moderately vulnerable to compaction. The problem is not limited to crop land or forest areas (especially because of non-site adjusted harvesting machines) but is also prevalent in rangelands and grassland, and even in so called natural non-disturbed systems. The main reasons for an intense increase in compacted agricultural or forested regions are the still increasing masses of the machines as well the increased frequency of wheeling under non favorable site conditions. Shear and vibration induced soil deformation enhances the deterioration of soil properties especially if the soil water content is very high and the internal soil strength very low. The same is true for animal trampling in combination with overgrazing of moist to wet pastures which subsequently causes a denser (i.e. reduced proportion of coarse pores with smaller continuity) but still structured soil horizons and will finally end in a compacted platy structure. In combination with high water content and shearing due to trampling therefore results in a complete muddy homogeneous soil with no structure at all. (Krümmelbein et al. 2013) Site managements of arable, forestry or horticulture soils requires a sufficiently rigid pore system which guarantees water, gas and heat exchange, nutrient transport and adsorption as well as an optimal rootability in order to avoid subsoil compaction. Such pore system also guarantees a sufficient microbial activity and composition in order to also decompose the plant etc. debris. It is therefore essential that well structured horizons dominate in soils with at best subangular blocky structure or in the top A- horizons a crumbly structure due to biological activity. In contrast defines the formation of a platy structure down to deeper depth and/or in combination with the deterioration of a continuous pore system an intensely degraded soil. A dominating anisotropy of pore functions causes a lateral soil and water movement. Doerner and Horn (2006), documented the increasing effect of stress and shear affected horizontal anisotropy on the hydraulic and gas permeability which coincides with a retarded gas exchange and an increased proportion of e.g. CO2 or even CH4 in soil pores and hinders the normal population growth. If the internal soil strength is exceeded the microbial composition and activity is converted to anoxia and even results in the emission of CH4 (Haas et al. 2016). Furthermore, the accessibility of nutrient adsorption places as well as connection between the pores within the compacted soils is decreased and results in a retarded ion mass flow and diffusion within the plats and /or in between the soil horizons. How to overcome these negative effects and how to deal with soils adequately according to their internal strength will be presented in the lecture - we need to improve the food production at an preserved land area for growing population. Literature Haas,C., Holthusen,D., Mordhorst,A., Lipiec,J., Horn, R. 2016. Elastic and plastic soil deformation and its influence on emission of greenhouse gases. Int. Agrophys., 30, 173-184 Krümmelbein, J., R.Horn 2013: Cycle of Soil Structure. Soil Degradation 183-198, Advances in Geoecology, 42, Catena Verlag, ISBN: 978-3-923381-59-3

USDA-ARS?s Scientific Manuscript database

Ecosystems that maximize soil organic matter and good soil structure maintain high soil biological functioning, soil health and plant growth. Natural ecosystems such as prairies are valuable benchmarks for developing sustainable crop and soil management practices. Soil biological properties critical...

Slumping in the rain - winter soil structure across Scotland and its physical degradation from extreme weather

NASA Astrophysics Data System (ADS)

Hall, Rebecca; Hallett, Paul; Raffan, Annette; Lilly, Allan; Baggaley, Nikki; Rowan, John; Crookes, Bill; Ball, Bruce

2017-04-01

Scotland is blessed with fertile and resilient soils that produce great cereal yields and whisky. However, there is worrying anecdotal evidence, confirmed by a small body of science, that some farming practices are causing widespread physical degradation of these soils. Studies from other UK regions have identified soil physical degradation by compaction, unstable seedbeds and erosion as a moderate to serious problem, depending on farming practice, soil properties and climate. In 2015/2016 we sampled 120 fields from 4 catchments in Scotland to describe the state of soil structure in the winter. To obtain a rapid assessment, we used the increasingly popular and easily interpretable Visual Evaluations of Soil Structure (VESS) and Subsoil Structure (SubVESS). We found severe soil structural degradation in 18% of topsoils and 9% of subsoils for 120 fields in 4 catchments. The severe 2015/2016 winter precipitation, the worst ever recorded, caused a 30% increase in occurrence of severely degraded topsoils, as determined from sampling some of the same fields before and after this unprecedented weather event. Run-off, erosion and nutrient losses were about 10X from degraded parts of fields such as tramlines than either within the field or at less trafficked boundaries. There was some agreement between areas identified as structurally degraded and those ranked as being susceptible to topsoil compaction using a simple model. Broad scale surveys that incorporate temporal sampling, such as the study reported here, are essential to provide regional assessments of soil degradation and to inform follow-on, targeted studies, where more in-depth analysis would be feasible.

Soil processes and functions across an international network of Critical Zone Observatories: Introduction to experimental methods and initial results

NASA Astrophysics Data System (ADS)

Banwart, Steven; Menon, Manoj; Bernasconi, Stefano M.; Bloem, Jaap; Blum, Winfried E. H.; Souza, Danielle Maia de; Davidsdotir, Brynhildur; Duffy, Christopher; Lair, Georg J.; Kram, Pavel; Lamacova, Anna; Lundin, Lars; Nikolaidis, Nikolaos P.; Novak, Martin; Panagos, Panos; Ragnarsdottir, Kristin Vala; Reynolds, Brian; Robinson, David; Rousseva, Svetla; de Ruiter, Peter; van Gaans, Pauline; Weng, Liping; White, Tim; Zhang, Bin

2012-11-01

Growth in human population and demand for wealth creates ever-increasing pressure on global soils, leading to soil losses and degradation worldwide. Critical Zone science studies the impact linkages between these pressures, the resulting environmental state of soils, and potential interventions to protect soil and reverse degradation. New research on soil processes is being driven by the scientific hypothesis that soil processes can be described along a life cycle of soil development. This begins with formation of new soil from parent material, development of the soil profile, and potential loss of the developed soil functions and the soil itself under overly intensive anthropogenic land use, thus closing the cycle. Four Critical Zone Observatories in Europe have been selected focusing research at sites that represent key stages along the hypothetical soil life cycle; incipient soil formation, productive use of soil for farming and forestry, and decline of soil due to longstanding intensive agriculture. Initial results from the research show that soil develops important biogeochemical properties on the time scale of decades and that soil carbon and the development of favourable soil structure takes place over similar time scales. A new mathematical model of soil aggregate formation and degradation predicts that set-aside land at the most degraded site studied can develop substantially improved soil structure with the accumulation of soil carbon over a period of several years. Further results demonstrate the rapid dynamics of soil carbon; how quickly it can be lost, and also demonstrate how data from the CZOs can be used to determine parameter values for models at catchment scale. A structure for a new integrated Critical Zone model is proposed that combines process descriptions of carbon and nutrient flows, a simplified description of the soil food web, and reactive transport; all coupled with a dynamic model for soil structure and soil aggregation. This approach is proposed as a methodology to analyse data along the soil life cycle and test how soil processes and rates vary within, and between, the CZOs representing different life cycle stages. In addition, frameworks are discussed that will help to communicate the results of this science into a more policy relevant format using ecosystem service approaches.

Estimating soil erosion risk and evaluating erosion control measures for soil conservation planning at Koga watershed in the highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Molla, Tegegne; Sisheber, Biniam

2017-01-01

Soil erosion is one of the major factors affecting sustainability of agricultural production in Ethiopia. The objective of this paper is to estimate soil erosion using the universal soil loss equation (RUSLE) model and to evaluate soil conservation practices in a data-scarce watershed region. For this purpose, soil data, rainfall, erosion control practices, satellite images and topographic maps were collected to determine the RUSLE factors. In addition, measurements of randomly selected soil and water conservation structures were done at three sub-watersheds (Asanat, Debreyakob and Rim). This study was conducted in Koga watershed at upper part of the Blue Nile basin which is affected by high soil erosion rates. The area is characterized by undulating topography caused by intensive agricultural practices with poor soil conservation practices. The soil loss rates were determined and conservation strategies have been evaluated under different slope classes and land uses. The results showed that the watershed is affected by high soil erosion rates (on average 42 t ha-1 yr-1), greater than the maximum tolerable soil loss (18 t ha-1 yr-1). The highest soil loss (456 t ha-1 yr-1) estimated from the upper watershed occurred on cultivated lands of steep slopes. As a result, soil erosion is mainly aggravated by land-use conflicts and topographic factors and the rugged topographic land forms of the area. The study also demonstrated that the contribution of existing soil conservation structures to erosion control is very small due to incorrect design and poor management. About 35 % out of the existing structures can reduce soil loss significantly since they were constructed correctly. Most of the existing structures were demolished due to the sediment overload, vulnerability to livestock damage and intense rainfall. Therefore, appropriate and standardized soil and water conservation measures for different erosion-prone land uses and land forms need to be implemented in Koga watershed.

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

PubMed

Mendes, Lucas William; Tsai, Siu Mui

2018-01-01

Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

Impact of Hydrologic Variability on Ecosystem Dynamics and the Sustainable Use of Soil and Water Resources

NASA Astrophysics Data System (ADS)

Porporato, A. M.

2013-05-01

We discuss the key processes by which hydrologic variability affects the probabilistic structure of soil moisture dynamics in water-controlled ecosystems. These in turn impact biogeochemical cycling and ecosystem structure through plant productivity and biodiversity as well as nitrogen availability and soil conditions. Once the long-term probabilistic structure of these processes is quantified, the results become useful to understand the impact of climatic changes and human activities on ecosystem services, and can be used to find optimal strategies of water and soil resources management under unpredictable hydro-climatic fluctuations. Particular applications regard soil salinization, phytoremediation and optimal stochastic irrigation.

Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review.

PubMed

Zhu, Xiaomin; Chen, Baoliang; Zhu, Lizhong; Xing, Baoshan

2017-08-01

Biochars have attracted tremendous attention due to their effects on soil improvement; they enhance carbon storage, soil fertility and quality, and contaminant (organic and heavy metal) immobilization and transformation. These effects could be achieved by modifying soil microbial habitats and (or) directly influencing microbial metabolisms, which together induce changes in microbial activity and microbial community structures. This review links microbial responses, including microbial activity, community structures and soil enzyme activities, with changes in soil properties caused by biochars. In particular, we summarized possible mechanisms that are involved in the effects that biochar-microbe interactions have on soil carbon sequestration and pollution remediation. Special attention has been paid to biochar effects on the formation and protection of soil aggregates, biochar adsorption of contaminants, biochar-mediated transformation of soil contaminants by microorganisms, and biochar-facilitated electron transfer between microbial cells and contaminants and soil organic matter. Certain reactive organic compounds and heavy metals in biochar may induce toxicity to soil microorganisms. Adsorption and hydrolysis of signaling molecules by biochar interrupts microbial interspecific communications, potentially altering soil microbial community structures. Further research is urged to verify the proposed mechanisms involved in biochar-microbiota interactions for soil remediation and improvement. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Microbiome Structure of Oklahoma Cropland and Prairie Soils and its Response to Seasonal Forcing and Management Practices

NASA Astrophysics Data System (ADS)

Cornell, C. R.; Peterson, B.; Zhou, J.; Xiao, X.; Wawrik, B.

2017-12-01

Greenhouse gases (GHG) emissions from soils are primarily the consequence of microbial processes. Agricultural management of soils is known to affect the structure of microbial communities, and it is likely that dominant GHG emitting microbial activities are impacted via requisite practices. To gain better insight into the impact of seasonal forcing and management practices on the microbiome structure in Oklahoma agricultural soils, a seasonal study was conducted. Over a year period, samples were collected bi-weekly during wet months, and monthly during dry months from two grassland and two managed agricultural sites in El Reno, Oklahoma. Microbial community structure was determined in quadruplicate for each site and time point via 16S rRNA gene sequencing. Measures of soil water content, subsoil nitrate, ammonium, organic matter, total nitrogen, and biomass were also taken for each time point. Data analysis revealed several important trends, indicating greater microbial diversity in native grassland and distinct microbial community changes in response to management practices. The native grassland soils also contained greater microbial biomass than managed soils and both varied in response to rainfall events. Native grassland soils harbor more diverse microbial communities, with the diversity and biomass decreasing along a gradient of agricultural management intensity. These data indicate that microbial community structure in El Reno soils occurs along a continuum in which native grasslands and highly managed agricultural soils (tilling and manure application) form end members. Integration with measurements from eddy flux towers into modelling efforts using the DeNitrification-DeComposition (DNDC) model is currently being explored to improve predictions of GHG emissions from grassland soils.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bond-Lamberty, Benjamin; Bolton, Harvey; Fansler, Sarah J.

The effects of climate change on soil organic matter—its structure, microbial community, carbon storage, and respiration response—remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampledmore » the original 1994 soil transplants and controls, measuring CO 2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5 °C monthly maximum air temperature, +50 mm yr -1precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. Lastly, these results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.« less

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak.

PubMed

Pec, Gregory J; Karst, Justine; Taylor, D Lee; Cigan, Paul W; Erbilgin, Nadir; Cooke, Janice E K; Simard, Suzanne W; Cahill, James F

2017-01-01

Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Land application of tylosin and chlortetracycline swine manure: Impacts to soil nutrients and soil microbial community structure.

PubMed

Stone, James J; Dreis, Erin K; Lupo, Christopher D; Clay, Sharon A

2011-01-01

The land application of aged chortetracycle (CTC) and tylosin-containing swine manure was investigated to determine associated impacts to soil microbial respiration, nutrient (phosphorus, ammonium, nitrate) cycling, and soil microbial community structure under laboratory conditions. Two silty clay loam soils common to southeastern South Dakota were used. Aerobic soil respiration results using batch reactors containing a soil-manure mixture showed that interactions between soil, native soil microbial populations, and antimicrobials influenced CO(2) generation. The aged tylosin treatment resulted in the greatest degree of CO(2) inhibition, while the aged CTC treatment was similar to the no-antimicrobial treatment. For soil columns in which manure was applied at a one-time agronomic loading rate, there was no significant difference in soil-P behavior between either aged CTC or tylosin and the no-antimicrobial treatment. For soil-nitrogen (ammonium and nitrate), the aged CTC treatment resulted in rapid ammonium accumulation at the deeper 40cm soil column depth, while nitrate production was minimal. The aged CTC treatment microbial community structure was different than the no-antimicrobial treatment, where amines/amide and carbohydrate chemical guilds utilization profile were low. The aged tylosin treatment also resulted in ammonium accumulation at 40 cm column depth, however nitrate accumulation also occurred concurrently at 10 cm. The microbial community structure for the aged tylosin was also significantly different than the no-antimicrobial treatment, with a higher degree of amines/amides and carbohydrate chemical guild utilization compared to the no-antimicrobial treatment. Study results suggest that land application of CTC and tylosin-containing manure appears to fundamentally change microbial-mediated nitrogen behavior within soil A horizons.

[Fractal features of soil aggregate structure in slope farmland with different de-farming patterns in South Sichuan Province of China].

PubMed

Wang, Jing-Yan; Hu, Ting-Xing; Gong, Wei; Gong, Yuan-Bo; Luo, Cheng-De

2010-06-01

By using fractal model, this paper studied the fractal dimension of soil aggregate structure (D) in the slope farmland (CK), its 5-year de-farmed Neosinocalamus affinis plantation (NAP), Bambusa pervariabilis x Dendrocalamopsis oldhami plantation (BDP), Alnus crenastogyne + Neosinocalamus affinis plantation (ANP), and abandoned farmland (AFL) in south Sichuan Province of China, and analyzed the relationships between the D and soil physical and chemical properties. In the de-farmed plantations and abandoned farmland, the contents of > 0.25 mm soil aggregates and water-stable aggregates were increased significantly, compared with those in the slope farmland. The D was 1.377-2.826, being in the order of NAP < BDP < ANP < AFL < CK, and decreased with the increasing contents of > 0.25 mm soil aggregates and water-stable aggregates. Comparing with CK, de-farming increased the soil natural water content, capillary porosity, and contents of soil organic matter, total N, alkali-hydrolysable N, total P, and total K, and decreased soil bulk density, non-capillary porosity, and aeration porosity. There were close relationships between the fractal dimension of soil aggregate structure and the soil physical and chemical properties. All the results suggested that the de-farming of slope farmland was beneficial to the increase of the contents of > 0.25 mm soil aggregates and water-stable aggregates, and the enhancement of soil structure stability. The D could be used as an ideal index to evaluate soil fertility, and planting Neosinocalamus affinis on the de-farming slope farmland was a good measure for the improvement of soil fertility in the research area.

Microbial community structure and activity in trace element-contaminated soils phytomanaged by Gentle Remediation Options (GRO).

PubMed

Touceda-González, M; Prieto-Fernández, Á; Renella, G; Giagnoni, L; Sessitsch, A; Brader, G; Kumpiene, J; Dimitriou, I; Eriksson, J; Friesl-Hanl, W; Galazka, R; Janssen, J; Mench, M; Müller, I; Neu, S; Puschenreiter, M; Siebielec, G; Vangronsveld, J; Kidd, P S

2017-12-01

Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR. Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg -1 soil, respiration increased from 7.4 to 40.1 mg C-CO 2 kg -1 soil d -1 , and enzyme activities were 2-11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reflecting on the structure of soil classification systems: insights from a proposal for integrating subsoil data into soil information systems

NASA Astrophysics Data System (ADS)

Dondeyne, Stefaan; Juilleret, Jérôme; Vancampenhout, Karen; Deckers, Jozef; Hissler, Christophe

2017-04-01

Classification of soils in both World Reference Base for soil resources (WRB) and Soil Taxonomy hinges on the identification of diagnostic horizons and characteristics. However as these features often occur within the first 100 cm, these classification systems convey little information on subsoil characteristics. An integrated knowledge of the soil, soil-to-substratum and deeper substratum continuum is required when dealing with environmental issues such as vegetation ecology, water quality or the Critical Zone in general. Therefore, we recently proposed a classification system of the subsolum complementing current soil classification systems. By reflecting on the structure of the subsoil classification system which is inspired by WRB, we aim at fostering a discussion on some potential future developments of WRB. For classifying the subsolum we define Regolite, Saprolite, Saprock and Bedrock as four Subsolum Reference Groups each corresponding to different weathering stages of the subsoil. Principal qualifiers can be used to categorize intergrades of these Subsoil Reference Groups while morphologic and lithologic characteristics can be presented with supplementary qualifiers. We argue that adopting a low hierarchical structure - akin to WRB and in contrast to a strong hierarchical structure as in Soil Taxonomy - offers the advantage of having an open classification system avoiding the need for a priori knowledge of all possible combinations which may be encountered in the field. Just as in WRB we also propose to use principal and supplementary qualifiers as a second level of classification. However, in contrast to WRB we propose to reserve the principal qualifiers for intergrades and to regroup the supplementary qualifiers into thematic categories (morphologic or lithologic). Structuring the qualifiers in this manner should facilitate the integration and handling of both soil and subsoil classification units into soil information systems and calls for paying attention to these structural issues in future developments of WRB.

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

PubMed Central

Zhen, Zhen; Liu, Haitao; Wang, Na; Guo, Liyue; Meng, Jie; Ding, Na; Wu, Guanglei; Jiang, Gaoming

2014-01-01

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils. PMID:25302996

Response of soil microbial activities and microbial community structure to vanadium stress.

PubMed

Xiao, Xi-Yuan; Wang, Ming-Wei; Zhu, Hui-Wen; Guo, Zhao-Hui; Han, Xiao-Qing; Zeng, Peng

2017-08-01

High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC 50 ) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

Assessing the performance of structure-from-motion photogrammetry and terrestrial lidar 1 at reconstructing soil surface microtopography of naturally vegetated plots

USDA-ARS?s Scientific Manuscript database

Soil microtopography or soil roughness is a property of critical importance in many earth surface processes but is often difficult to measure. Advances in computer vision technologies have made image-based 3D depiction of the soil surface or Structure-from-Motion (SfM) available to many scientists ...

The Role of Teak Leaves (Tectona grandis), Rhizobium, and Vesicular-Arbuscular Mycorrhizae on Improving Soil Structure and Soil Nutrition

NASA Astrophysics Data System (ADS)

Yuliani; Rahayu, Y. S.

2018-01-01

Calcium is the largest mineral in calcareous soils. High levels of calcium carbonate lead to phosphate deposition. Nutrient deficiencies in calcareous soil (mainly Phosphate and Nitrogen) resulted only certain crops with a wide range of tolerances that can grow. Meanwhile, dynamics nutrient in calcareous soils also depend on the topography and decomposition of the litter in the growing vegetation. The purpose of this study was to describe the pattern of nutrient enhancement and soil-texture structures on calcareous soils after littering the teak leaves, Rhizobium and Vesicular Arbuscular Mycorrhiza. The research parameters were the concentration of N, P, K; C/N ratio, humid acid content, and soil structure, which measured at days 30, 60, and 85 of soil decomposition process. The results showed that at days 30, the texture and structure of the soil tend to be stable (porosity 31.2, DMR 1.93, moisture content 0.36, sandy clay) while at days 85 has been very stable (porosity 49.8; Water content 0.28, sandy clay). While C and N organic, N and K concentration at days 30 showed low value (C organic 1.03, N 0.12, K 0.49, C / N ratio 9). This condition is almost unchanged at days 85. While the P value shows very high value (60.53) at days 30 although after 60 days the P content showed a decrease.

Analysing Structure Dynamics in Arable Soils using X-ray Micro-Tomography

NASA Astrophysics Data System (ADS)

Schlüter, S.; Weller, U.; Vogel, H.-J.

2009-04-01

Structure is a dynamic property of soil. It interacts with many biotic and abiotic features and controls various soil functions. We analyzed soil structure within different plots of the ''Static Fertilisation Experiment'' at the agricultural research station in Bad Lauchstaedt (Germany) using X-ray micro tomography. The aim was to investigate in how far different levels of organic carbon, increased microbial activity and enhanced plant growth affects structural properties of an arable soil. Since 106 years one plot has experienced a constant application of farmyard manure and fertilisers, whereas the other has never been fertilised in this period. Intact soil cores from the chernozem soil at the two plots were taken from a depth of 5 to 15 cm (Ap-horizon) and 35 to 45 cm (Ah-horizon) to analyse structural changes with depth and in two different seasons (spring and summer) to investigate structure dynamics. The pore structure was analysed by quantifying the mean geometrical and topological characteristics of the pore network as a function of pore size. This was done by a combination of Minkowski functionals and morphological size distibution. For small structural features close to the image resolution the results clearly depend on the applied filtering technique and segmentation thresholds. Therefore the application of different image enhancement techniques is discussed. Furthermore, a new method for an automated determination of grey value thesholds for the segmentation of CT-images into pore space and solid is developed and evaluated. We highlight the relevance of image resolution for structure analysis. Results of the structure analysis reveal that the spring samples of the ploughed layer (Ap-horizon) from the fertilised plot have significantly higher macroporosities (P < 0.05) than those from the non-fertilised plot. The internal connectivity of the pore network is better in the fertilised plot and the pore size distribution was found to be different, too. The differences in porosity and pore connectivity increase from spring to summer. Both plots were compacted by a rolling machine in late winter. So the difference in structure dynamics is interpreted as an enhanced structure resiliency in the fertilised and carbon enriched plot after that compaction. A comparison with porosity features of a nearby reference profil under grassland demonstrates that the impact of tillage on pore structure is higher than the different contents in organic carbon. The carbon enriched horizon beneath the ploughed layer (Ah-horizon) shows no differences in pore size distribution and connectivity as a function of fertilisation. Thus, at that soil depth, no long-term effects of fertilization in terms of soil structure are detectable. Obviously, the highly different energy input during 106 years only affects the structure of the top soil.

Earthquake Ground Motion Selection

DOT National Transportation Integrated Search

2012-05-01

Nonlinear analyses of soils, structures, and soil-structure systems offer the potential for more accurate characterization of geotechnical and structural response under strong earthquake shaking. The increasing use of advanced performance-based desig...

Effect of soil structure on the growth of bacteria in soil quantified using CARD-FISH

NASA Astrophysics Data System (ADS)

Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Otten, Wilfred

2014-05-01

It has been reported that compaction of soil due to use of heavy machinery has resulted in the reduction of crop yield. Compaction affects the physical properties of soil such as bulk density, soil strength and porosity. This causes an alteration in the soil structure which limits the mobility of nutrients, water and air infiltration and root penetration in soil. Several studies have been conducted to explore the effect of soil compaction on plant growth and development. However, there is scant information on the effect of soil compaction on the microbial community and its activities in soil. Understanding the effect of soil compaction on microbial community is essential as microbial activities are very sensitive to abrupt environmental changes in soil. Therefore, the aim of this work was to investigate the effect of soil structure on growth of bacteria in soil. The bulk density of soil was used as a soil physical parameter to quantify the effect of soil compaction. To detect and quantify bacteria in soil the method of catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used. This technique results in high intensity fluorescent signals which make it easy to quantify bacteria against high levels of autofluorescence emitted by soil particles and organic matter. In this study, bacterial strains Pseudomonas fluorescens SBW25 and Bacillus subtilis DSM10 were used. Soils of aggregate size 2-1mm were packed at five different bulk densities in polyethylene rings (4.25 cm3).The soil rings were sampled at four different days. Results showed that the total number of bacteria counts was reduced significantly (P

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystemmore » scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.« less

Spatial variability structure of soil CO2 emission and soil physical and chemical properties characterized by fractal dimension in sugarcane areas

NASA Astrophysics Data System (ADS)

Bicalho, E. S.; Teixeira, D. B.; Panosso, A. R.; Perillo, L. I.; Iamaguti, J. L.; Pereira, G. T.; La Scala, N., Jr.

2012-04-01

Soil CO2 emission (FCO2) is influenced by chemical, physical and biological factors that affect the production of CO2 in the soil and its transport to the atmosphere, varying in time and space depending on environmental conditions, including the management of agricultural area. The aim of this study was to investigate the structure of spatial variability of FCO2 and soil properties by using fractal dimension (DF), derived from isotropic variograms at different scales, and construction of fractograms. The experimental area consisted of a regular grid of 60 × 60 m on sugarcane area under green management, containing 141 points spaced at minimum distances ranging from 0.5 to 10 m. Soil CO2 emission, soil temperature and soil moisture were evaluated over a period of 7 days, and soil chemical and physical properties were determined by sampling at a depth of 0.0 to 0.1 m. FCO2 showed an overall average of 1.51 µmol m-2 s-1, correlated significantly (p < 0.05) with soil physical factors such as soil bulk density, air-filled pore space, macroporosity and microporosity. Significant DF values were obtained in the characterization of FCO2 in medium and large scales (from 20 m). Variations in DF with the scale, which is the fractogram, indicate that the structure of FCO2 variability is similar to that observed for the soil temperature and total pore volume, and reverse for the other soil properties, except for macroporosity, sand content, soil organic matter, carbon stock, C/N ratio and CEC, which fractograms were not significantly correlated to the FCO2 fractogram. Thus, the structure of spatial variability for most soil properties, characterized by fractogram, presents a significant relationship with the structure of spatial variability of FCO2, generally with similar or dissimilar behavior, indicating the possibility of using the fractogram as tool to better observe the behavior of the spatial dependence of the variables along the scale.

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation.

PubMed

Koebernick, Nicolai; Daly, Keith R; Keyes, Samuel D; George, Timothy S; Brown, Lawrie K; Raffan, Annette; Cooper, Laura J; Naveed, Muhammad; Bengough, Anthony G; Sinclair, Ian; Hallett, Paul D; Roose, Tiina

2017-10-01

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high-resolution (c. 5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8 d in microcosms packed with sandy loam soil at 1.2 g cm -3 dry bulk density. Root hairs were visualised within air-filled pore spaces, but not in the fine-textured soil regions. We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (> 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image-based modelling. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

X-ray microtomography analysis of soil structure deformation caused by centrifugation

NASA Astrophysics Data System (ADS)

Schlüter, Steffen; Leuther, Frederic; Vogler, Steffen; Vogel, Hans-Jörg

2016-04-01

Centrifugation provides a fast method to measure soil water retention curves over a wide moisture range. However, deformation of soil structure may occur at high angular velocities in the centrifuge. The objective of this study was to capture these changes in soil structure with X-ray microtomography and to measure local deformations via digital volume correlation. Two samples were investigated that differ in texture and rock content. A detailed analysis of the pore space reveals an interplay between shrinkage due to drying and soil compaction due to compression. Macroporosity increases at moderate angular velocity because of crack formation due to moisture release. At higher angular velocities, corresponding to capillary pressure of <-100kPa, macroporosity decreases again because of structure deformation due to compression. While volume changes due to swelling clay minerals are immanent to any drying process, the compaction of soil is a specific drawback of the centrifugation method. A new protocol for digital volume correlation was developed to analyze the spatial heterogeneity of deformation. In both samples the displacement of soil constituents is highest in the top part of the sample and exhibits high lateral variability explained by the spatial distribution of macropores in the sample. Centrifugation should therefore only be applied after the completion of all other hydraulic or thermal experiments, or any other analysis that depends on the integrity of soil structure.

X-ray microtomography analysis of soil structure deformation caused by centrifugation

NASA Astrophysics Data System (ADS)

Schlüter, S.; Leuther, F.; Vogler, S.; Vogel, H.-J.

2016-01-01

Centrifugation provides a fast method to measure soil water retention curves over a wide moisture range. However, deformation of soil structure may occur at high angular velocities in the centrifuge. The objective of this study was to capture these changes in soil structure with X-ray microtomography and to measure local deformations via digital volume correlation. Two samples were investigated that differ in texture and rock content. A detailed analysis of the pore space reveals an interplay between shrinkage due to drying and soil compaction due to compression. Macroporosity increases at moderate angular velocity because of crack formation due to moisture release. At higher angular velocities, corresponding to capillary pressure of ψ < -100 kPa, macroporosity decreases again because of structure deformation due to compression. While volume changes due to swelling clay minerals are immanent in any drying process, the compaction of soil is a specific drawback of the centrifugation method. A new protocol for digital volume correlation was developed to analyze the spatial heterogeneity of deformation. In both samples the displacement of soil constituents is highest in the top part of the sample and exhibits high lateral variability explained by the spatial distribution of macropores in the sample. Centrifugation should therefore only be applied after the completion of all other hydraulic or thermal experiments, or any other analysis that depends on the integrity of soil structure.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem.

PubMed

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2015-03-20

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

Influence of Soil Properties on Soldierless Termite Distribution.

PubMed

Bourguignon, Thomas; Drouet, Thomas; Šobotník, Jan; Hanus, Robert; Roisin, Yves

2015-01-01

In tropical rainforests, termites constitute an important part of the soil fauna biomass, and as for other soil arthropods, variations in soil composition create opportunities for niche partitioning. The aim of this study was twofold: first, we tested whether soil-feeding termite species differ in the foraging substrate; second, we investigated whether soil-feeding termites select their foraging sites to enhance nutrients intake. To do so, we collected termites and analysed the composition and structure of their feeding substrates. Although Anoplotermes-group members are all considered soil-feeders, our results show that some species specifically feed on abandoned termite nests and very rotten wood, and that this substrate selection is correlated with previous stable isotope analyses, suggesting that one component of niche differentiation among species is substrate selection. Our results show that the composition and structure of bare soils on which different termite species foraged do not differ, suggesting that there is no species specialization for a particular type of bare soil. Finally, the bare soil on which termites forage does not differ from random soil samples. Overall, our results suggest that few species of the Anoplotermes-group are specialized toward substrates rich in organic matter, but that the vast majority forage on soil independently of its structural and chemical composition, being ecologically equivalent for this factor.

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan

NASA Astrophysics Data System (ADS)

Pershina, E. V.; Ivanova, E. A.; Nagieva, A. G.; Zhiengaliev, A. T.; Chirak, E. L.; Andronov, E. E.; Sergaliev, N. Kh.

2016-06-01

The goal of this study was to determine the relationships between the structure of the soil microbiome and the agroecological state of soils by the example of natural undisturbed (steppe areas) and anthropogenically disturbed (pastures, croplands, fallows) areas in the territory of northwestern Kazakhstan. The highest abundance of proteobacteria was found in the anthropogenically disturbed of fallows and in undisturbed soils; in other cases, actinobacteria and representatives of the Firmicutes phylum predominated. Different kinds of anthropogenic impacts resulted in the decrease in the portions of bacteria from the Acidobacteria, Gemmatimonadetes, and Firmicutes phyla. In the disturbed soils, the portions of bacteria from the Erysipelothrix, Mycobacterium, Methylibium, Skermanella, Ralstonia, Lactococcus, Bdellovibrio, Candidatus nitrososphaera, Catellatospora, Cellulomonas, Stenotrophomonas, and Steroidobacter genera increased. Bacteria of the Erysipelothrix and Methylibium genera occurred only in the undisturbed soils. The anthropogenically disturbed and undisturbed soils differed significantly in the taxonomic structure of their microbiomes forming two separate clusters, which confirms the efficiency of using the data on the structure of soil microbiomes when assessing the agroecological status of soils.

Land-use and soil depth affect resource and microbial stoichiometry in a tropical mountain rainforest region of southern Ecuador.

PubMed

Tischer, Alexander; Potthast, Karin; Hamer, Ute

2014-05-01

Global change phenomena, such as forest disturbance and land-use change, significantly affect elemental balances as well as the structure and function of terrestrial ecosystems. However, the importance of shifts in soil nutrient stoichiometry for the regulation of belowground biota and soil food webs have not been intensively studied for tropical ecosystems. In the present account, we examine the effects of land-use change and soil depth on soil and microbial stoichiometry along a land-use sequence (natural forest, pastures of different ages, secondary succession) in the tropical mountain rainforest region of southern Ecuador. Furthermore, we analyzed (PLFA-method) whether shifts in the microbial community structure were related to alterations in soil and microbial stoichiometry. Soil and microbial stoichiometry were affected by both land-use change and soil depth. After forest disturbance, significant decreases of soil C:N:P ratios at the pastures were followed by increases during secondary succession. Microbial C:N ratios varied slightly in response to land-use change, whereas no fixed microbial C:P and N:P ratios were observed. Shifts in microbial community composition were associated with soil and microbial stoichiometry. Strong positive relationships between PLFA-markers 18:2n6,9c (saprotrophic fungi) and 20:4 (animals) and negative associations between 20:4 and microbial N:P point to land-use change affecting the structure of soil food webs. Significant deviations from global soil and microbial C:N:P ratios indicated a major force of land-use change to alter stoichiometric relationships and to structure biological systems. Our results support the idea that soil biotic communities are stoichiometrically flexible in order to adapt to alterations in resource stoichiometry.

Factors Affecting Soil Microbial Community Structure in Tomato Cropping Systems

USDA-ARS?s Scientific Manuscript database

Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. We identified some of the most important factors controlling microbial biomass and community structure in an agroecosystem utilizing tomato plants with the following nine tre...

Faunal Drivers of Soil Flux Dynamics via Alterations in Crack Structure

NASA Astrophysics Data System (ADS)

DeCarlo, Keita; Caylor, Kelly

2016-04-01

Organismal activity, in addition to its role in ecological feedbacks, has the potential to serve as instigators or enhancers of atmospheric and hydrologic processes via alterations in soil structural regimes. We investigated the biomechanical effect of faunal activity on soil carbon dynamics via changes in soil crack structure, focusing on three dryland soil systems: bioturbated, biocompacted and undisturbed soils. Carbon fluxes were characterized using a closed-system respiration chamber, with CO2 concentration differences measured using an infrared gas analyzer (IRGA). Results show that faunal influences play a divergent biomechanics role in bulk soil cracking: bioturbation induced by belowground fauna creates "surficial" (shallow, large, well-connected) networks relative to the "systematic" (deep, moderate, poorly connected) networks created by aboveground fauna. The latter also shows a "memory" of past wetting/drying events in the consolidated soil through a crack layering effect. These morphologies further drive differences in soil carbon flux: under dry conditions, bioturbated and control soils show a persistently high and low mean carbon flux, respectively, while biocompacted soils show a large diurnal trend, with daytime lows and nighttime highs comparable to the control and bioturbated soils, respectively. Overall fluxes under wet conditions are considerably higher, but also more variable, though higher mean fluxes are observed in the biocompacted and bioturbated soils. Our results suggest that the increased surface area in the bioturbated soils create enhanced but constant diffusive processes, whereas the increased thermal gradient in the biocompacted soils create novel convective processes that create high fluxes that are diurnal in nature.

Impacts of soil moisture content on visual soil evaluation

NASA Astrophysics Data System (ADS)

Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Bondi, Giulia; Creamer, Rachel; Holden, Nick

2017-04-01

Visual Soil Examination and Evaluation (VSE) techniques offer tools for soil quality assessment. They involve the visual and tactile assessment of soil properties such as aggregate size and shape, porosity, redox morphology, soil colour and smell. An increasing body of research has demonstrated the reliability and utility of VSE techniques. However a number of limitations have been identified, including the potential impact of soil moisture variation during sampling. As part of a national survey of grassland soil quality in Ireland, an evaluation of the impact of soil moisture on two widely used VSE techniques was conducted. The techniques were Visual Evaluation of Soil Structure (VESS) (Guimarães et al., 2011) and Visual Soil Assessment (VSA) (Shepherd, 2009). Both generate summarising numeric scores that indicate soil structural quality, though employ different scoring mechanisms. The former requires the assessment of properties concurrently and the latter separately. Both methods were deployed on 20 sites across Ireland representing a range of soils. Additional samples were taken for soil volumetric water (θ) determination at 5-10 and 10-20 cm depth. No significant correlation was observed between θ 5-10 cm and either VSE technique. However, VESS scores were significantly related to θ 10-20 cm (rs = 0.40, sig = 0.02) while VSA scores were not (rs = -0.33, sig = 0.06). VESS and VSA scores can be grouped into quality classifications (good, moderate and poor). No significant mean difference was observed between θ 5-10 cm or θ 10-20 cm according to quality classification by either method. It was concluded that VESS scores may be affected by soil moisture variation while VSA appear unaffected. The different scoring mechanisms, where the separate assessment and scoring of individual properties employed by VSA, may limit soil moisture effects. However, moisture content appears not to affect overall structural quality classification by either method. References Guimarães, R.M.C., Ball, B.C. & Tormena, C.A. 2011. Improvements in the visual evaluation of soil structure, Soil Use and Management, 27, 3: 395-403 Shepherd, G.T. 2009. Visual Soil Assessment. Field guide for pastoral grazing and cropping on flat to rolling country. 2nd edn. Horizons regional council, New Zealand.

The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry.

PubMed

Liu, Shanshan; Wang, Feng; Xue, Kai; Sun, Bo; Zhang, Yuguang; He, Zhili; Van Nostrand, Joy D; Zhou, Jizhong; Yang, Yunfeng

2015-03-01

Soil transplant into warmer regions has been shown to alter soil microbiology. In contrast, little is known about the effects of soil transplant into colder regions, albeit that climate cooling has solicited attention in recent years. To address this question, we transplanted bare fallow soil over large transects from southern China (subtropical climate zone) to central (warm temperate climate zone) and northern China (cold temperate climate zone). After an adaptation period of 4 years, soil nitrogen components, microbial biomass and community structures were altered. However, the effects of soil transplant on microbial communities were dampened by maize cropping, unveiling a negative interaction between cropping and transplant. Further statistical analyses with Canonical correspondence analysis and Mantel tests unveiled annual average temperature, relative humidity, aboveground biomass, soil pH and NH4 (+) -N content as environmental attributes closely correlated with microbial functional structures. In addition, average abundances of amoA-AOA (ammonia-oxidizing archaea) and amoA-AOB (ammonia-oxidizing bacteria) genes were significantly (P < 0.05) correlated with soil nitrification capacity, hence both AOA and AOB contributed to the soil functional process of nitrification. These results suggested that the soil nitrogen cycle was intimately linked with microbial community structure, and both were subjected to disturbance by soil transplant to colder regions and plant cropping. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Changes in soil microbial community structure influenced by agricultural management practices in a mediterranean agro-ecosystem.

PubMed

García-Orenes, Fuensanta; Morugán-Coronado, Alicia; Zornoza, Raul; Cerdà, Artemi; Scow, Kate

2013-01-01

Agricultural practices have proven to be unsuitable in many cases, causing considerable reductions in soil quality. Land management practices can provide solutions to this problem and contribute to get a sustainable agriculture model. The main objective of this work was to assess the effect of different agricultural management practices on soil microbial community structure (evaluated as abundance of phospholipid fatty acids, PLFA). Five different treatments were selected, based on the most common practices used by farmers in the study area (eastern Spain): residual herbicides, tillage, tillage with oats and oats straw mulching; these agricultural practices were evaluated against an abandoned land after farming and an adjacent long term wild forest coverage. The results showed a substantial level of differentiation in the microbial community structure, in terms of management practices, which was highly associated with soil organic matter content. Addition of oats straw led to a microbial community structure closer to wild forest coverage soil, associated with increases in organic carbon, microbial biomass and fungal abundances. The microbial community composition of the abandoned agricultural soil was characterised by increases in both fungal abundances and the metabolic quotient (soil respiration per unit of microbial biomass), suggesting an increase in the stability of organic carbon. The ratio of bacteria:fungi was higher in wild forest coverage and land abandoned systems, as well as in the soil treated with oat straw. The most intensively managed soils showed higher abundances of bacteria and actinobacteria. Thus, the application of organic matter, such as oats straw, appears to be a sustainable management practice that enhances organic carbon, microbial biomass and activity and fungal abundances, thereby changing the microbial community structure to one more similar to those observed in soils under wild forest coverage.

Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.

PubMed

Fall, S; Nazaret, S; Chotte, J L; Brauman, A

2004-08-01

The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites ( Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

This report was prepared at the request of the Lawrence Livermore Laboratory (LLL) to provide background information for analyzing soil-structure interaction by the frequency-independent impedance function approach. LLL is conducting such analyses as part of its seismic review of selected operating plants under the Systematic Evaluation Program for the US Nuclear Regulatory Commission. The analytical background and basic assumptionsof the impedance function theory are briefly reviewed, and the role of radiation damping in soil-structure interaction analysis is discussed. The validity of modeling soil-structure interaction by using frequency-independent functions is evaluated based on data from several field tests. Finally, the recommendedmore » procedures for performing soil-structure interaction analyses are discussed with emphasis on the modal superposition method.« less

State-Space Estimation of Soil Organic Carbon Stock

NASA Astrophysics Data System (ADS)

Ogunwole, Joshua O.; Timm, Luis C.; Obidike-Ugwu, Evelyn O.; Gabriels, Donald M.

2014-04-01

Understanding soil spatial variability and identifying soil parameters most determinant to soil organic carbon stock is pivotal to precision in ecological modelling, prediction, estimation and management of soil within a landscape. This study investigates and describes field soil variability and its structural pattern for agricultural management decisions. The main aim was to relate variation in soil organic carbon stock to soil properties and to estimate soil organic carbon stock from the soil properties. A transect sampling of 100 points at 3 m intervals was carried out. Soils were sampled and analyzed for soil organic carbon and other selected soil properties along with determination of dry aggregate and water-stable aggregate fractions. Principal component analysis, geostatistics, and state-space analysis were conducted on the analyzed soil properties. The first three principal components explained 53.2% of the total variation; Principal Component 1 was dominated by soil exchange complex and dry sieved macroaggregates clusters. Exponential semivariogram model described the structure of soil organic carbon stock with a strong dependence indicating that soil organic carbon values were correlated up to 10.8m.Neighbouring values of soil organic carbon stock, all waterstable aggregate fractions, and dithionite and pyrophosphate iron gave reliable estimate of soil organic carbon stock by state-space.

78 FR 13097 - Electric Power Research Institute; Seismic Evaluation Guidance

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-26

... outcrop motion for which the soil layers above the foundation elevation have been removed. Updating the... performing soil-structure interaction analyses. Consistent with guidance described in DC/COL-ISG-017, ``Ensuring Hazard-Consistent Seismic Input for Site Response and Soil Structure Interaction Analyses,'' the...

Three Soil Quality Demonstrations for Educating Extension Clientele

ERIC Educational Resources Information Center

Hoorman, James J.

2014-01-01

There is a renewed interest in educating youth, Master Gardeners, and agricultural producers about soil quality. Three soil demonstrations show how soil organic matter increases water holding capacity, improves soil structure, and increases nutrient retention. Exercise one uses clay bricks and sponges to represent mineral soils and soil organic…

Soil and Water: Some Teaching Suggestions.

ERIC Educational Resources Information Center

Fischer, Richard B.

1987-01-01

Outlines six soil and water investigations that students can pursue outdoors, in nature centers, or in classrooms: soil characteristics; relationship between soil ph and plant life; what aggregates tell us; differences in soil structure; differences in rate of water absorption by soil; and soil exploration with a Berlesi funnel. (NEC)

Environmental impacts of different crop rotations in terms of soil compaction.

PubMed

Götze, Philipp; Rücknagel, Jan; Jacobs, Anna; Märländer, Bernward; Koch, Heinz-Josef; Christen, Olaf

2016-10-01

Avoiding soil compaction caused by agricultural management is a key aim of sustainable land management, and the soil compaction risk should be considered when assessing the environmental impacts of land use systems. Therefore this project compares different crop rotations in terms of soil structure and the soil compaction risk. It is based on a field trial in Germany, in which the crop rotations (i) silage maize (SM) monoculture, (ii) catch crop mustard (Mu)_sugar beet (SB)-winter wheat (WW)-WW, (iii) Mu_SM-WW-WW and (iv) SB-WW-Mu_SM are established since 2010. Based on the cultivation dates, the operation specific soil compaction risks and the soil compaction risk of the entire crop rotations are modelled at two soil depths (20 and 35 cm). To this end, based on assumptions of the equipment currently used in practice by a model farm, two scenarios are modelled (100 and 50% hopper load for SB and WW harvest). In addition, after one complete rotation, in 2013 and in 2014, the physical soil parameters saturated hydraulic conductivity (kS) and air capacity (AC) were determined at soil depths 2-8, 12-18, 22-28 and 32-38 cm in order to quantify the soil structure. At both soil depths, the modelled soil compaction risks for the crop rotations including SB (Mu_SB-WW-WW, SB-WW-Mu_SM) are higher (20 cm: medium to very high risks; 35 cm: no to medium risks) than for those without SB (SM monoculture, Mu_SM-WW-WW; 20 cm: medium risks; 35 cm: no to low risks). This increased soil compaction risk is largely influenced by the SB harvest in years where soil water content is high. Halving the hopper load and adjusting the tyre inflation pressure reduces the soil compaction risk for the crop rotation as a whole. Under these conditions, there are no to low soil compaction risks for all variants in the subsoil (soil depth 35 cm). Soil structure is mainly influenced in the topsoil (2-8 cm) related to the cultivation of Mu as a catch crop and WW as a preceding crop. Concerning kS, Mu_SB-WW-WW (240 cm d(-1)) and Mu_SM-WW-WW (196 cm d(-1)) displayed significantly higher values than the SM monoculture (67 cm d(-1)), indicating better structural stability and infiltration capacity. At other soil depths, and for the parameter AC, there are no systematic differences in soil structure between the variants. Under the circumstances described, all crop rotations investigated are not associated with environmental impacts caused by soil compaction. Copyright © 2016 Elsevier Ltd. All rights reserved.

Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.

PubMed

Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

2012-07-01

Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.

Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau

PubMed Central

Li, Yuntao; Adams, Jonathan; Shi, Yu; Wang, Hao; He, Jin-Sheng; Chu, Haiyan

2017-01-01

Global change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community. Bacterial and eukaryotic diversity was quite stable among different soil water availability, but archaeal diversity was dramatically different between the habitats. The auxotype of methanogens also varied significantly among different habitats. The co-varying soil properties among habitats shaped the community structure of soil microbes, with archaea being particularly sensitive in terms of community composition, diversity and functional groups. Bacterial and archaeal phylogenetic community turnover was mainly driven by deterministic processes while stochastic processes had stronger effects on eukaryotic phylogenetic community turnover. Our work provides insight into microbial community, functional group and phylogenetic turnover under different soil conditions in low-latitude alpine ecosystem. PMID:28401921

Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Li, Yuntao; Adams, Jonathan; Shi, Yu; Wang, Hao; He, Jin-Sheng; Chu, Haiyan

2017-04-01

Global change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community. Bacterial and eukaryotic diversity was quite stable among different soil water availability, but archaeal diversity was dramatically different between the habitats. The auxotype of methanogens also varied significantly among different habitats. The co-varying soil properties among habitats shaped the community structure of soil microbes, with archaea being particularly sensitive in terms of community composition, diversity and functional groups. Bacterial and archaeal phylogenetic community turnover was mainly driven by deterministic processes while stochastic processes had stronger effects on eukaryotic phylogenetic community turnover. Our work provides insight into microbial community, functional group and phylogenetic turnover under different soil conditions in low-latitude alpine ecosystem.

Jatropha curcas L. Root Structure and Growth in Diverse Soils

PubMed Central

Valdés-Rodríguez, Ofelia Andrea; Sánchez-Sánchez, Odilón; Pérez-Vázquez, Arturo; Caplan, Joshua S.; Danjon, Frédéric

2013-01-01

Unlike most biofuel species, Jatropha curcas has promise for use in marginal lands, but it may serve an additional role by stabilizing soils. We evaluated the growth and structural responsiveness of young J. curcas plants to diverse soil conditions. Soils included a sand, a sandy-loam, and a clay-loam from eastern Mexico. Growth and structural parameters were analyzed for shoots and roots, although the focus was the plasticity of the primary root system architecture (the taproot and four lateral roots). The sandy soil reduced the growth of both shoot and root systems significantly more than sandy-loam or clay-loam soils; there was particularly high plasticity in root and shoot thickness, as well as shoot length. However, the architecture of the primary root system did not vary with soil type; the departure of the primary root system from an index of perfect symmetry was 14 ± 5% (mean ± standard deviation). Although J. curcas developed more extensively in the sandy-loam and clay-loam soils than in sandy soil, it maintained a consistent root to shoot ratio and root system architecture across all types of soil. This strong genetic determination would make the species useful for soil stabilization purposes, even while being cultivated primarily for seed oil. PMID:23844412

Jatropha curcas L. root structure and growth in diverse soils.

PubMed

Valdés-Rodríguez, Ofelia Andrea; Sánchez-Sánchez, Odilón; Pérez-Vázquez, Arturo; Caplan, Joshua S; Danjon, Frédéric

2013-01-01

Unlike most biofuel species, Jatropha curcas has promise for use in marginal lands, but it may serve an additional role by stabilizing soils. We evaluated the growth and structural responsiveness of young J. curcas plants to diverse soil conditions. Soils included a sand, a sandy-loam, and a clay-loam from eastern Mexico. Growth and structural parameters were analyzed for shoots and roots, although the focus was the plasticity of the primary root system architecture (the taproot and four lateral roots). The sandy soil reduced the growth of both shoot and root systems significantly more than sandy-loam or clay-loam soils; there was particularly high plasticity in root and shoot thickness, as well as shoot length. However, the architecture of the primary root system did not vary with soil type; the departure of the primary root system from an index of perfect symmetry was 14 ± 5% (mean ± standard deviation). Although J. curcas developed more extensively in the sandy-loam and clay-loam soils than in sandy soil, it maintained a consistent root to shoot ratio and root system architecture across all types of soil. This strong genetic determination would make the species useful for soil stabilization purposes, even while being cultivated primarily for seed oil.

Relationship between the erosion properties of soils and other parameters

USDA-ARS?s Scientific Manuscript database

Soil parameters are essential for erosion process prediction and ultimately improved model development, especially as they relate to dam and levee failure. Soil parameters including soil texture and structure, soil classification, soil compaction, moisture content, and degree of saturation can play...

Calibrating Nonlinear Soil Material Properties for Seismic Analysis Using Soil Material Properties Intended for Linear Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spears, Robert Edward; Coleman, Justin Leigh

2015-08-01

Seismic analysis of nuclear structures is routinely performed using guidance provided in “Seismic Analysis of Safety-Related Nuclear Structures and Commentary (ASCE 4, 1998).” This document, which is currently under revision, provides detailed guidance on linear seismic soil-structure-interaction (SSI) analysis of nuclear structures. To accommodate the linear analysis, soil material properties are typically developed as shear modulus and damping ratio versus cyclic shear strain amplitude. A new Appendix in ASCE 4-2014 (draft) is being added to provide guidance for nonlinear time domain SSI analysis. To accommodate the nonlinear analysis, a more appropriate form of the soil material properties includes shear stressmore » and energy absorbed per cycle versus shear strain. Ideally, nonlinear soil model material properties would be established with soil testing appropriate for the nonlinear constitutive model being used. However, much of the soil testing done for SSI analysis is performed for use with linear analysis techniques. Consequently, a method is described in this paper that uses soil test data intended for linear analysis to develop nonlinear soil material properties. To produce nonlinear material properties that are equivalent to the linear material properties, the linear and nonlinear model hysteresis loops are considered. For equivalent material properties, the shear stress at peak shear strain and energy absorbed per cycle should match when comparing the linear and nonlinear model hysteresis loops. Consequently, nonlinear material properties are selected based on these criteria.« less

Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

NASA Astrophysics Data System (ADS)

Cao, Chengyou; Zhang, Ying; Qian, Wei; Liang, Caiping; Wang, Congmin; Tao, Shuang

2017-10-01

The conversion of natural grassland into agricultural fields is an intensive anthropogenic perturbation commonly occurring in semiarid regions, and this perturbation strongly affects soil microbiota. In this study, the influences of land-use conversion on the soil properties and bacterial communities in the Horqin Grasslands in Northeast China were assessed. This study aimed to investigate (1) how the abundances of soil bacteria changed across land-use types, (2) how the structure of the soil bacterial community was altered in each land-use type, and (3) how these variations were correlated with soil physical and chemical properties. Variations in the diversities and compositions of bacterial communities and the relative abundances of dominant taxa were detected in four distinct land-use systems, namely, natural meadow grassland, paddy field, upland field, and poplar plantation, through the high-throughput Illumina MiSeq sequencing technique. The results indicated that land-use changes primarily affected the soil physical and chemical properties and bacterial community structure. Soil properties, namely, organic matter, pH, total N, total P, available N and P, and microbial biomass C, N, and P, influenced the bacterial community structure. The dominant phyla and genera were almost the same among the land-use types, but their relative abundances were significantly different. The effects of land-use changes on the structure of soil bacterial communities were more quantitative than qualitative.

The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau.

PubMed

Zhang, Xinfang; Xu, Shijian; Li, Changming; Zhao, Lin; Feng, Huyuan; Yue, Guangyang; Ren, Zhengwei; Cheng, Guogdong

2014-01-01

In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM>M>S>DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.

PubMed

Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

2015-01-01

The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.

Effects of Cd and Pb on soil microbial community structure and activities.

PubMed

Khan, Sardar; Hesham, Abd El-Latif; Qiao, Min; Rehman, Shafiqur; He, Ji-Zheng

2010-02-01

Soil contamination with heavy metals occurs as a result of both anthropogenic and natural activities. Heavy metals could have long-term hazardous impacts on the health of soil ecosystems and adverse influences on soil biological processes. Soil enzymatic activities are recognized as sensors towards any natural and anthropogenic disturbance occurring in the soil ecosystem. Similarly, microbial biomass carbon (MBC) is also considered as one of the important soil biological activities frequently influenced by heavy metal contamination. The polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) has recently been used to investigate changes in soil microbial community composition in response to environmental stresses. Soil microbial community structure and activities are difficult to elucidate using single monitoring approach; therefore, for a better insight and complete depiction of the soil microbial situation, different approaches need to be used. This study was conducted in a greenhouse for a period of 12 weeks to evaluate the changes in indigenous microbial community structure and activities in the soil amended with different application rates of Cd, Pb, and Cd/Pb mix. In a field environment, soil is contaminated with single or mixed heavy metals; so that, in this research, we used the selected metals in both single and mixed forms at different application rates and investigated their toxic effects on microbial community structure and activities, using soil enzyme assays, plate counting, and advanced molecular DGGE technique. Soil microbial activities, including acid phosphatase (ACP), urease (URE), and MBC, and microbial community structure were studied. A soil sample (0-20 cm) with an unknown history of heavy metal contamination was collected and amended with Cd, Pb, and Cd/Pb mix using the CdSO(4) and Pb(NO(3))(2) solutions at different application rates. The amended soils were incubated in the greenhouse at 25 +/- 4 degrees C and 60% water-holding capacity for 12 weeks. During the incubation period, samples were collected from each pot at 0, 2, 9, and 12 weeks for enzyme assays, MBC, numeration of microbes, and DNA extraction. Fumigation-extraction method was used to measure the MBC, while plate counting techniques were used to numerate viable heterotrophic bacteria, fungi, and actinomycetes. Soil DNAs were extracted from the samples and used for DGGE analysis. ACP, URE, and MBC activities of microbial community were significantly lower (p < 0.05) in the metal-amended samples than those in the control. The enzyme inhibition extent was obvious between different incubation periods and varied as the incubation proceeded, and the highest rate was detected in the samples after 2 weeks. However, the lowest values of ACP and URE activities (35.6% and 36.6% of the control, respectively) were found in the Cd(3)/Pb(3)-treated sample after 2 weeks. Similarly, MBC was strongly decreased in both Cd/Pb-amended samples and highest reduction (52.4%) was detected for Cd(3)/Pb(3) treatment. The number of bacteria and actinomycetes were significantly decreased in the heavy metal-amended samples compared to the control, while fungal cells were not significantly different (from 2.3% to 23.87%). In this study, the DGGE profile indicated that the high dose of metal amendment caused a greater change in the number of bands. DGGE banding patterns confirmed that the addition of metals had a significant impact on microbial community structure. In soil ecosystem, heavy metals exhibit toxicological effects on soil microbes which may lead to the decrease of their numbers and activities. This study demonstrated that toxicological effects of heavy metals on soil microbial community structure and activities depend largely on the type and concentration of metal and incubation time. The inhibition extent varied widely among different incubation periods for these enzymes. Furthermore, the rapid inhibition in microbial activities such as ACP, URE, and MBC were observed in the 2 weeks, which should be related to the fact that the microbes were suddenly exposed to heavy metals. The increased inhibition of soil microbial activities is likely to be related to tolerance and adaptation of the microbial community, concentration of pollutants, and mechanisms of heavy metals. The DGGE profile has shown that the structure of the bacterial community changed in amended heavy metal samples. In this research, the microbial community structure was highly affected, consistent with the lower microbial activities in different levels of heavy metals. Furthermore, a great community change in this study, particularly at a high level of contamination, was probably a result of metal toxicity and also unavailability of nutrients because no nutrients were supplied during the whole incubation period. The added concentrations of heavy metals have changed the soil microbial community structure and activities. The highest inhibitory effects on soil microbial activities were observed at 2 weeks of incubation. The bacteria were more sensitive than actinomycetes and fungi. The DGGE profile indicated that bacterial community structure was changed in the Cd/Pb-amended samples, particularly at high concentrations. The investigation of soil microbial community structure and activities together could give more reliable and accurate information about the toxic effects of heavy metals on soil health.

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

PubMed Central

Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

2015-01-01

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

Land-use and land-management change: relationships with earthworm and fungi communities and soil structural properties.

PubMed

Spurgeon, David J; Keith, Aidan M; Schmidt, Olaf; Lammertsma, Dennis R; Faber, Jack H

2013-12-01

Change in land use and management can impact massively on soil ecosystems. Ecosystem engineers and other functional biodiversity in soils can be influenced directly by such change and this in turn can affect key soil functions. Here, we employ meta-analysis to provide a quantitative assessment of the effects of changes in land use and land management across a range of successional/extensification transitions (conventional arable → no or reduced tillage → grassland → wooded land) on community metrics for two functionally important soil taxa, earthworms and fungi. An analysis of the relationships between community change and soil structural properties was also included. Meta-analysis highlighted a consistent trend of increased earthworm and fungal community abundances and complexity following transitions to lower intensity and later successional land uses. The greatest changes were seen for early stage transitions, such as introduction of reduced tillage regimes and conversion to grassland from arable land. Not all changes, however, result in positive effects on the assessed community metrics. For example, whether woodland conversion positively or negatively affects community size and complexity depends on woodland type and, potentially, the changes in soil properties, such as pH, that may occur during conversion. Alterations in soil communities tended to facilitate subsequent changes in soil structure and hydrology. For example, increasing earthworm abundances and functional group composition were shown to be positively correlated with water infiltration rate (dependent on tillage regime and habitat characteristics); while positive changes in fungal biomass measures were positively associated with soil microaggregate stability. These findings raise the potential to manage landscapes to increase ecosystem service provision from soil biota in relation to regulation of soil structure and water flow.

Slow reaction of soil structure to conservation agriculture practices in Veneto silty soils (North-Easter Italy)

NASA Astrophysics Data System (ADS)

Piccoli, Ilaria; Camarotto, Carlo; Lazzaro, Barbara; Furlan, Lorenzo; Morari, Francesco

2017-04-01

Soil structure plays a pivotal role in soil functioning and can inform of the degradation of the soil ecosystem. Intensive and repeated tillage operations have been known to negatively affect the soil structure characteristics while conservation agriculture (CA) practices were demonstrated to improve soil structure and related ecosystem services. The aim of this study is to evaluate the effect of conservation agriculture practices on total porosity, pore size distribution, pore architecture and morphology on silty soils of Veneto low-lying plain (North-Eastern Italy). Experimental design was established in 2010 on 4 farms in North-Eastern Italy to compare conventional intensive tillage system "IT" versus conservation agriculture "CA" (no-tillage, cover-crop and residue retention). 96 samples were collected in 2015 at four depths down to 50 cm depth, and investigated for porosity from micro to macro by coupling mercury intrusion porosimetry (MIP) (0.0074-100 µm) and x-ray computed microtomography (µCT) (>26 µm). Pore morphology and architecture were studied from 3D images analysis and MIP pore size curve. Ultramicroporosity class (0.1-5 μm) positively responded to CA after 5-yr of practices adoption while no significant effects were observed in the x-ray µCT domain (> 26 µm). Silty soils of Veneto plain showed a slow reaction to conservation agriculture because of the low soil organic carbon content and poor aggregate stability. Nevertheless the positive influence of CA on ultramicroporosity, which is strictly linked to soil organic carbon (SOC) stabilization, indicated that a virtuous cycle was initiated between SOC and porosity, hopefully leading to well-developed macropore systems and, in turn, enhanced soil functions and ecosystem services.

Similar soil microbial community structure across different environments after long-term succession: evidence from volcanoes of different ages.

PubMed

Xu, Shangqi; Zhang, Jianfeng; Luo, Shasha; Zhou, Xue; Shi, Shaohua; Tian, Chunjie

2018-06-08

Soil microbes play critical roles in global biogeochemical cycles, but their succession patterns across long temporal scales have rarely been studied. In this study, soil samples were collected from three volcanoes in Wudalianchi, northeastern China: Laoheishan (LH, approximately 240 years old), Dongjiaodebushan (DJ, 0.45-0.6 million years old), and Nangelaqiushan (NG, 0.8-1.3 million years old). For each volcano, both southern (S) and northern (N) slope aspects were sampled. Soil microbial communities were analyzed using phospholipid fatty acid analysis (PLFA). The results showed that soil properties and microbial biomass changed perceptibly among different volcanoes and different slope aspects. Almost all of the detected soil nutrient contents of LH were lowest, and total microbial biomass of LH was 40 and 36% lower than those of NG and DJ, respectively. LH was significantly different from NG and DJ in soil microbial community structure with a higher relative abundance of fungi and a lower relative abundance of actinomycetes and bacteria. However, for the two ancient volcanoes (NG and DJ), soil microbial community structures were highly similar among different ages and different slope aspects. No difference was detected in any of the measured microbial indices, including richness, evenness, Shannon's diversity, Simpson's diversity and the relative abundance of different microbial groups. The results indicated that while soil microbial biomass may change across different soil environments after long-term succession, soil microbial community structure can remain relatively stable. The results further indicated that soil microbes may show different successional patterns in different stages of succession. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

HYDRAULIC REDISTRIBUTION OF SOIL WATER BY ROOTS IN FORESTS OF THE PACIFIC NORTHWEST

EPA Science Inventory

One aspect of structural complexity of forest canopies is the root system structure belowground, which influences patterns of soil water utilization by trees. Deeply rooted trees and other plants can hydraulically lift water via their roots from several m below the soil surface ...

Visualization of soil structure and pore structure modifications by pioneering ground beetles (Cicindelidae) in surface sediments of an artificial catchment

NASA Astrophysics Data System (ADS)

Badorreck, Annika; Gerke, Horst H.; Weller, Ulrich; Vontobel, Peter

2010-05-01

An artificial catchment was constructed to study initial soil and ecosystem development. As a key process, the pore structure dynamics in the soil at the surface strongly influences erosion, infiltration, matter dynamics, and vegetation establishment. Little is known, however, about the first macropore formation in the very early stage. This presentation focuses on observations of soil pore geometry and its effect on water flow at the surface comparing samples from three sites in the catchment and in an adjacent "younger" site composed of comparable sediments. The surface soil was sampled in cylindrical plastic rings (10 cm³) down to 2 cm depth in three replicates each site and six where caves from pioneering ground-dwelling beetles Cicindelidae were found. The samples were scanned with micro-X-ray computed tomography (at UFZ-Halle, Germany) with a resolution of 0.084 mm. The infiltration dynamics were visualized with neutronradiography (at Paul-Scherer-Institute, Switzerland) on slab-type soil samples in 2D. The micro-tomographies exhibit formation of surface sealing whose thickness and intensity vary with silt and clay content. The CT images show several coarser- and finer-textured micro-layers at the sample surfaces that were formed as a consequence of repeated washing in of finer particles in underlying coarser sediment. In micro-depressions, the uppermost layers consist of sorted fine sand and silt due to wind erosion. Similar as for desert pavements, a vesicular pore structure developed in these sediments on top, but also scattered in fine sand- and silt-enriched micro-layers. The ground-dwelling activity of Cicindelidae beetles greatly modifies the soil structure through forming caves in the first centimetres of the soil. Older collapsed caves, which form isolated pores within mixed zones, were also found. The infiltration rates were severely affected both, by surface crusts and activity of ground-dwelling beetles. The observations demonstrate relatively high abiotic and biotic dynamics of soil pore structure in the soil surface even during the very early development stages. The structure formation has potentially great effects on changing runoff and infiltration by forming sealing layers or preferential flow paths.

Influence of Precipitation Regime on Microbial Decomposition Patterns in Semi-Arid Ecosystems

NASA Astrophysics Data System (ADS)

Feris, K. P.; Jilek, C.; Huber, D. P.; Reinhardt, K.; deGraaff, M.; Lohse, K.; Germino, M.

2011-12-01

In water-limited semi-arid sagebrush steppe ecosystems predicted changes in climate may manifest as a shift from historically winter/snow-dominated precipitation regimes to one dominated by spring rains. In these ecosystems soil microorganisms play a vital role in linking the effects of water availability and plant productivity to biogeochemical cycling. Patterns of soil microbial catalyzed organic matter decomposition patters (i.e. patterns of extracellular enzyme activity (EEA)) are thought to depend upon the quantity and quality of soil organic matter (SOM), pH, and mean annual precipitation (Sinsabaugh, 2008), and less on the timing and magnitude of precipitation. However, sagebrush-steppe plant communities respond strongly to changes in the timing and magnitude of precipitation, and preliminary findings by our group suggest that corresponding changes in SOM quantity, quality, N-cycle dynamics, and soil structure are occurring. Therefore, we hypothesized: 1) Shifts in the timing and magnitude of precipitation would indirectly affect soil microbial decomposition patterns via responses in the plant community structure; and 2) Changes in precipitation patterns can directly affect soil microbial community structure and function, in effect uncoupling the interaction between plant community structure and soil community structure. We tested our hypotheses by determining the influence of experimentally manipulated timing and magnitude of precipitation on soil microbial EEA using standard flourometric assays in soils sampled under plant canopies and plant interspaces. We assessed this response in a mature (18 + years) ecohydrologic field experiment in eastern Idaho that annually imitates three possible post climatic-shift precipitation regimes (Ambient (AMB): no additional precipitation, ~200mm annually; Summer (SUMM): 200mm provisioned at 50mm bi-weekly starting in June; and Fall/Spring (F/S): 200mm provisioned over 1-2 weeks in October or April) (n=3). Within plant interspaces Beta glucosaminide activity increased by 18% in treatments receiving additional F/S precipitation, whereas alpha glucopyranoside activity was lower in the F/S and SUMM plots. Conversely, underplant canopies alpha glucopyranoside activity increased by 15% in the SUMM and F/S precipitation treatments. Across treatments and sampling types (i.e. plant canopy vs. interspace), cellobioside activity levels are consistently elevated in response to additional precipitation compared to those of the control plots. When coupled with recent preliminary findings by our group regarding changes in plant and microbial community structure and SOM, C-storage, and soil structural responses, these preliminary findings suggest that 1) microbial community structure and function respond both directly and indirectly to changes in climate, and 2) thus provide a mechanism for changes in plant community structure to feed-forward to affect soil carbon decomposition patterns and ultimately soil carbon storage potential.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem

PubMed Central

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D.; Zhou, Jizhong

2015-01-01

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0–5 cm and 5–15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems. PMID:25791904

[Effects of grape-replanting on soil bacterial and fungal populations].

PubMed

Li, Kun; Guo, Xiu-wu; Sun, Ying-ni; Zhang, Li-heng; Hu, Xi-xi

2009-12-01

Rhizosphere and non-rhizosphere soil samples were collected from the vineyards having been planted for 3 and 30 years, and PCR-DGGE technique was adopted to study the effects of grape-replanting on the population structure and diversity of soil bacteria and fungi. The bacterial and fungal diversities were higher in 30-year-planted vineyard than in 3-year-planted vineyard, and higher in rhizosphere soil than in non-rhizosphere soil. After 30 years replanting, the population structure of bacteria and fungi approached the same in rhizosphere soil and non-rhizosphere soil but differed from that in fallow soil; while in the 3-year-planted vineyard, the population structure in rhizosphere soil was different from that in non-rhizosphere soil and fallow soil. Comparing with that in 3-year-planted vineyard, the rhizosphere soil microbial population in 30-year-planted vineyard had a greater change. In bacterial population, Flavobacterium sp. (DQ339585) and Bacillus sp. (AY039821) decreased while Pedobacter sp. (AJ871084) increased; in fungal population, Omphalina farinolens (EF413029) appeared, Pestalotiopsis sp. (DQ657877, DQ657875, DQ657871), Phacidium lacerum (DQ470976), and Lecythophora decumbens (AF353597) decreased, while Pilidium acerinum voucher (AY48709) increased. Bacillus sp., Flavobacterium sp. , and Pestalotiopsis sp. had antagonism to pathogen, and their decrease reduced the resistance of grape against pathogen. The increase of Pilidium acerinum voucher might relate to the severe disease after grape-replanting.

Vertical variation of a black soil's properties in response to freeze-thaw cycles and its links to shift of microbial community structure.

PubMed

Han, Ziming; Deng, Mingwen; Yuan, Anqi; Wang, Jiahui; Li, Hao; Ma, Jincai

2018-06-01

Soil freeze-thaw cycles (FTCs) change soil physical, chemical, and biological properties, however information regarding their vertical variations in response to FTCs is limited. In this work, black soil (silty loam) packed soil columns were exposed to 8 FTCs, and soil properties were determined for each of vertical layer of soil columns. The results revealed that after FTCs treatment, moisture and electrical conductivity (EC) salinity tended to increase in upper soil layers. Increments of ammonium nitrogen (NH 4 + -N) and nitrate nitrogen (NO 3 - -N) in top layers (0-10cm) were greater than those in other layers, and increments of water soluble organic carbon (WSOC) and decrease of microbial biomass carbon (MBC) in middle layers (10-20cm) were greater than those in both ends. Overall, microbial community structure was mainly influenced by soil physical properties (moisture and EC) and chemical properties (pH and WSOC). For bacterial (archaeal) and fungal communities, soil physical properties, chemical properties and their interaction explained 79.73% and 82.66% of total variation, respectively. Our results provided insights into the vertical variation of soil properties caused by FTCs, and such variation had a major impact on the change of structure and composition of soil bacterial and fungal communities. Copyright © 2017 Elsevier B.V. All rights reserved.

Microbial diversity affects self-organization of the soil–microbe system with consequences for function

PubMed Central

Crawford, John W.; Deacon, Lewis; Grinev, Dmitri; Harris, James A.; Ritz, Karl; Singh, Brajesh K.; Young, Iain

2012-01-01

Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits. PMID:22158839

Simazine biodegradation and community structures of ammonia-oxidizing microorganisms in bioaugmented soil: impact of ammonia and nitrate nitrogen sources.

PubMed

Wan, Rui; Yang, Yuyin; Sun, Weimin; Wang, Zhao; Xie, Shuguang

2014-02-01

The objective of the present study was to investigate the impact of ammonia and nitrate nitrogen sources on simazine biodegradation by Arthrobacter sp. strain SD1 and the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in non-agricultural soil. Soil microcosms with different treatments were constructed for herbicide biodegradation test. The relative abundance of the strain SD1 and the structures of AOA and AOB communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. The co-existence of two inorganic nitrogen sources (ammonia and nitrate) had certain impact on simazine dissipation by the strain SD1. Bioaugmentation could induce a shift in the community structures of both AOA and AOB, but AOA were more responsive. Nitrogen application had significant impacts on AOA and AOB communities in bioaugmented soils. Moreover, in non-bioaugmented soil, the community structure of AOA, instead of AOB, could be quickly recovered after herbicide application. This study could add some new insights towards the impacts of nitrogen sources on s-triazine bioremediation and ammonia-oxidizing microorganisms in soil ecosystem.

Soils and public health: the vital nexus

NASA Astrophysics Data System (ADS)

Pachepsky, Yakov

2015-04-01

Soils sustain life. They affect human health via quantity, quality, and safety of available food and water, and via direct exposure of individuals to soils. Throughout the history of civilization, soil-health relationships have inspired spiritual movements, philosophical systems, cultural exchanges, and interdisciplinary interactions, and provided medicinal substances of paramount impact. Given the climate, resource, and population pressures, understanding and managing the soil-health interactions becomes a modern imperative. We are witnessing a paradigm shift from recognizing and yet disregarding the 'soil-health' nexus complexity to parameterizing this complexity and identifying reliable controls. This becomes possible with the advent of modern research tools as a source of 'big data' on multivariate nonlinear soil systems and the multiplicity of health metrics. The phenomenon of suppression of human pathogens in soils and plants presents a recent example of these developments. Evidence is growing about the dependence of pathogen suppression on the soil microbial community structure which, in turn, is affected by the soil-plant system management. Soil eutrophication appears to create favorable conditions for pathogen survival. Another example of promising information-rich research considers links and feedbacks between the soil microbial community structure and structure of soil physical pore space. The two structures are intertwined and involved in the intricate self-organization that controls soil services to public health. This, in particular, affects functioning of soils as a powerful water filter and the capacity of this filter with respect to emerging contaminants in both 'green' and 'blue' waters. To evaluate effects of soil services to public health, upscaling procedures are needed for relating the fine-scale mechanistic knowledge to available coarse-scale information on soil properties and management. More needs to be learned about health effects of soils in organic agriculture that are often used for soil quality comparison and benchmarking. The influence of soil degradation and rehabilitation on public health has to be assessed in quantitative terms. Some links between soils and public health regarding, for example, immune maturation, antibiotic resistance development, and mental well-being, have been long hypothesized but remain to be examined. The data on soil-health relationships are scarce and very much disjointed, and a concerted international effort appears to be needed to encompass various economic and geographical settings. Current definitions of healthy soil broadly include aspects that are conducive for human health, and functional evaluation of soil quality with a focus on public health will have useful applications in public policies and perception. The 'soil-health' connection is complex in character, global in manifestation, and applicable to every human being.

Carbendazim induces a temporary change in soil bacterial community structure.

PubMed

Wang, Xiuguo; Song, Min; Gao, Chunming; Dong, Bin; Zhang, Qun; Fang, Hua; Yu, Yunlong

2009-01-01

The effect of carbendazim applications on the diversity and structure of a soil bacterial community was studied under field conditions using temperature gradient gel electrophoresis (TGGE) and partial sequence analysis of PCR-amplified 16S rRNA gene. After four successive introductions of carbendazim at a level of 0.94 kg active ingredient (a.i.)/ha, the genetic diversity (expressed as Shannon index, H') decreased from 1.43 in the control to 1.29 in treated soil. This harmful effect seems to increase with the concentration of carbendazim. The value of H' in the soil treated with carbendazim at 4.70 kg a.i./ha was reduced to 1.05 (P < or = 0.05). The structure of soil bacterial community was also affected after four repeated applications of carbendazim at levels of 0.94, 1.88 and 4.70 kg a.i./ha, as seen in the relative intensities of the individual band. However, the bacterial community in carbendazim-treated soil recovered to that in the control 360 d after the first treatment. The results indicated that repeated applications of carbendazim could reduce soil microbial diversity and alter the bacterial community structure temporarily.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation.

PubMed

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-07-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

PubMed Central

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-01-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant ‘seed bank'. PMID:25535940

Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils.

PubMed

Dai, Yu; Wu, Zhen; Zhou, Qiheng; Zhao, Qun; Li, Ningning; Xie, Shuguang; Liu, Yong

2015-10-01

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be involved in biotransformation of ammonia to nitrite in soil ecosystems. However, the distribution of AOA and AOB in plateau soils and influential factors remain largely unclear. In the present study, the activity, abundance and structure of ammonia oxidizers in different soils on the Yunnan Plateau were assessed using potential nitrification rates (PNRs), quantitative PCR assay and clone library analysis, respectively. Wide variation was found in both AOA and AOB communities in plateau soils. PNRs showed a significant positive correlation with AOB abundance. Both were determined by the ratio of organic carbon to nitrogen (C/N) and total phosphorous (TP). AOB could play a more important role in ammonia oxidation. AOB community diversity was likely affected by soil total nitrogen (TN) and total organic carbon (TOC) and was usually higher than AOA community diversity. Moreover, Nitrososphaera- and Nitrosospira-like organisms, respectively, were the dominant AOA and AOB in plateau soils. AOA community structure was likely shaped by TP and C/N, while AOB community structure was determined by pH. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

[Diversity and community structure of soil ammonia-oxidizing bacteria in Hulunbeier Grassland, Inner Mongolia].

PubMed

Wendu, Ri-le; Li, Gang; Yang, Dian-lin; Zhang, Jing-ni; Yi, Jin

2011-04-01

By the methods of polymerase chain reaction-denaturing gradient gel electrophoresis and sequence analysis, a comparative study was conducted on the diversity and community structure of soil ammonia-oxidizing bacteria in the Filifolium sibiricum steppe, Stipa baicalensis steppe, Leymus chinensis steppe, Stipa grandis steppe, and Stipa kryrowi steppe in Hulunbeier Grassland, Inner Mongolia. A significant difference was observed in the community structure of soil ammonia-oxidizing bacteria among the five steppes, with the similarity lower than 50%. The diversity of soil ammonia-oxidizing bacteria was the highest in F. sibiricum steppe, followed by in S. baicalensis steppe, L. chinensis steppe, S. kryrowi steppe, and S. grandis steppe. In the five steppes, Nitrosospira cluster 3 was the dominant group, and the Nitrosospira cluster 1, 2, and 4 as well as Nitrosomonas were also found. The community structure of soil ammonia oxidizing bacteria in F. sibiricum steppe was most complex, while that in L. chinensis steppe and S. grandis steppe was relatively simple. Correlation analysis indicated that there existed significant positive correlations between the diversity of soil ammonia-oxidizing bacteria and the soil moisture, total nitrogen, total organic carbon, and C/N ratio (P<0.05).

Impact of land-use and long-term (>150 years) charcoal accumulation on microbial activity, biomass and community structure in temperate soils (Belgium).

NASA Astrophysics Data System (ADS)

Hardy, Brieuc; Cornelis, Jean-Thomas; Dufey, Joseph E.

2015-04-01

In the last decade, biochar has been increasingly investigated as a soil amendment for long-term soil carbon sequestration while improving soil fertility. On the short term, biochar application to soil generally increases soil respiration as well as microbial biomass and activity and affects significantly the microbial community structure. However, such effects are relatively short-term and tend to vanish over time. In our study, we investigated the long-term impact of charcoal accumulation and land-use on soil biota in temperate haplic Luvisols developed in the loess belt of Wallonia (Belgium). Charcoal-enriched soils were collected in the topsoil of pre-industrial (>150 years old) charcoal kilns in forest (4 sites) and cropland (5 sites). The topsoil of the adjacent charcoal-unaffected soils was sampled in a comparable way. Soils were characterized (pH, total, organic and inorganic C, total N, exchangeable Ca, Mg, K, Na, cation exchange capacity and available P) and natural soil organic matter (SOM) and black carbon (BC) contents were determined by differential scanning calorimetry. After rewetting at pF 2.5, soils were incubated during 140 days at 20 °C. At 70 days of incubation, 10 g of each soil were freeze dried in order to measure total microbial biomass and community structure by PLFA analysis. The PLFA dataset was analyzed by principal component analysis (PCA) while soil parameters were used as supplementary variables. For both agricultural and forest soils, the respiration rate is highly related to the total microbial biomass (R²=0.90). Both soil respiration and microbial biomass greatly depend on the SOM content, which indicates that the BC pool is relatively inert microbiologically. Land-use explains most of the variance in the PLFA dataset, largely governing the first principal component of the ACP. In forest soils, we observe a larger proportion of gram + bacteria, actinomycetes and an increased bacteria:fungi ratio compared to cropland, where gram - bacteria, arbuscular mycorrhizal fungi and 18:2 and 18:3 fungi are more present. BC is quite well represented (R=-0.765) by the third principal component of the PCA, representing 12.2 % of the total variance. It has limited impact on the community structure, particularly in cropland. However, in forest BC is negatively correlated (R=-0.785) with 18:1 fungi. The more pronounced effect of BC on community structure under forest could result from modified trophic conditions at kiln site (e.g. higher pH, lower available P content, …) while cultivation practices attenuated such differences over time in cropland. In conclusion, our survey tends to confirm that the influence of BC on the soil microbiological parameters is governed by indirect effects on trophic conditions. On the other hand, land-use affects dramatically soil microbial community structure.

A process-based framework for soil ecosystem services study and management.

PubMed

Su, Changhong; Liu, Huifang; Wang, Shuai

2018-06-15

Soil provides various indispensable ecosystem services for human society. Soil's complex structure and property makes the soil ecological processes complicated and brings about tough challenges for soil ecosystem services study. Most of the current frameworks on soil services focus exclusively on services per se, neglecting the links and underlying ecological mechanisms. This article put forward a framework on soil services by stressing the underlying soil mechanisms and processes, which includes: 1) analyzing soil natural capital stock based on soil structure and property, 2) disentangling the underlying complex links and soil processes, 3) soil services valuation based on field investigation and spatial explicit models, and 4) enacting soil management strategy based on soil services and their driving factors. By application of this framework, we assessed the soil services of sediment retention, water yield, and grain production in the Upper-reach Fenhe Watershed. Based on the ecosystem services and human driving factors, the whole watershed was clustered into five groups: 1) municipal area, 2) typical coal mining area, 3) traditional farming area, 4) unsustainable urbanizing area, and 5) ecological conservation area. Management strategies on soils were made according to the clustering based soil services and human activities. Copyright © 2018 Elsevier B.V. All rights reserved.

Pore-Scale Effects of Soil Structure And Microbial EPS Production On Soil Water Retention

NASA Astrophysics Data System (ADS)

Orner, E.; Anderson, E.; Rubinstein, R. L.; Chau, J. F.; Shor, L. M.; Gage, D. J.

2013-12-01

Climate-induced changes to the hydrological cycle will increase the frequency of extreme weather events including powerful storms and prolonged droughts. Moving forward, one of the major factors limiting primary productivity in terrestrial ecosystems will be sub-optimal soil moisture. We focus here on the ability of soils to retain moisture under drying conditions. A soil's ability to retain moisture is influenced by many factors including its texture, its structure, and the activities of soil microbes. In soil microcosms, the addition of small amounts of microbially-produced extracellular polymeric substances (EPS) can dramatically shift moisture retention curves. The objective of this research is to better understand how soil structure and EPS may act together to retain moisture in unsaturated soils. Replicate micromodels with exactly-conserved 2-D physical geometry were initially filled with aqueous suspensions of one of two types of bacteria: one mutant was ultra- muccoid and the other was non-muccoid. Replicate micromodels were held at a fixed, external, relative humidity, and the position of the air-water interface was imaged over time as water evaporates. There was no forced convection of air or water inside the micromodels: drying was achieved by water evaporation and diffusion alone. We used a fully automated, inverted microscope to image replicate drying lanes each with dimensions of 1 mm x 10 mm. A complete set of images was collected every 30 minutes for 30 hours. The results show devices loaded with the highly muccoid strain remained >40% hydrated for 13 h, while devices loaded with the non-muccoid remained >40% hydrated for only 6 h, and were completely dry by 13 h. Current work is comparing interfacial water fluxes in structured and unstructured settings, and is attempting to model the synergistic effects of soil structure and EPS content on moisture retention in real soils. This research may allow more accurate description of naturally-occurring feedbacks between the soil carbon and water cycles, and may enable agriculture biotechnology that enhances natural soil processes for improved resiliency of terrestrial ecosystems.

Using synthetic polymers to reduce soil erosion after forest fires in Mediterranean soils

NASA Astrophysics Data System (ADS)

Lado, Marcos; Ben-Hur, Meni; Inbar, Assaf

2010-05-01

Forest fires are a major environmental problem in the Mediterranean region because they result in a loss of vegetation cover, changes in biodiversity, increases in greenhouse gasses emission and a potential increase of runoff and soil erosion. The large increases in runoff and sediment yields after high severity fires have been attributed to several factors, among them: increase in soil water repellency; soil sealing by detached particles and by ash particles, and the loss of a surface cover. The presence of a surface cover increases infiltration, and decreases runoff and erosion by several mechanisms which include: rainfall interception, plant evapotranspiration, preservation of soil structure by increasing soil organic matter, and increasing surface roughness. The loss of vegetation cover as a result of fire leaves the surface of the soil exposed to the direct impact of the raindrops, and therefore the sensitivity of the soil to runoff generation and soil loss increases. In this work, we propose a new method to protect soils against post-fire erosion based on the application of synthetic polymers to the soil. Laboratory rainfall simulations and field runoff plots were used to analyze the suitability of the application of synthetic polymers to reduce soil erosion and stabilize soil structure in Mediterranean soils. The combination of these two processes will potentially favor a faster recovery of the vegetation structure. This method has been successfully applied in arable land, however it has not been tested in burnt forests. The outcome of this study may provide important managerial tools for forest management following fires.

[Distribution characteristics of soil nematodes in reclaimed land of copper-mine-tailings in different plant associations].

PubMed

Zhu, Yong-heng; Li, Ke-zhong; Zhang, Heng; Han, Fei; Zhou, Ju-hua; Gao, Ting-ting

2015-02-01

A survey was carried out to investigate soil nematode communities in the plant associations of gramineae (Arthraxon lanceolatus, AL; Imperata cylindrica, IC) and leguminosae (Glycine soja, GS) in reclaimed land of copper-mine-tailings and in the plant associations of gramineae (Digitaria chrysoblephara, DC-CK) of peripheral control in Fenghuang Mountain, Tongling City. A total of 1277 nematodes were extracted and sorted into 51 genera. The average individual density of the nematodes was 590 individuals · 100 g(-1) dry soil. In order to analyze the distribution character- istics of soil nematode communities in reclaimed land of copper-mine-tailings, Shannon community diversity index and soil food web structure indices were applied in the research. The results showed that the total number of nematode genus and the Shannon community diversity index of soil nematode in the three plant associations of AL, IC and GS were less than that in the plant associations of DC-CK. Compared with the ecological indices of soil nematode communities among the different plant associations in reclaimed land of copper-mine-tailings and peripheral natural habitat, we found that the structure of soil food web in the plant associations of GS was more mature, with bacterial decomposition being dominant in the soil organic matter decomposition, and that the soil ecosystem in the plant associations of GS was not stable with low interference. This indicated that the soil food web in the plant associations of leguminosae had a greater development potential to improve the ecological stability of the reclaimed land of copper-mine-tailings. On the other hand, the structure of soil food web in the plant associations of AL and IC were relatively stable in a structured state with fungal decomposition being dominant in the decomposition of soil organic matter. This indicated that the soil food web in the plant associations of gramineae was at a poor development level.

Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas.

PubMed

Carbonetto, Belén; Rascovan, Nicolás; Álvarez, Roberto; Mentaberry, Alejandro; Vázquez, Martin P

2014-01-01

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no-tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.

Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas

PubMed Central

Carbonetto, Belén; Rascovan, Nicolás; Álvarez, Roberto; Mentaberry, Alejandro; Vázquez, Martin P.

2014-01-01

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no- tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability. PMID:24923965

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses

PubMed Central

Zheng, Chengyu; Kang, Chunsheng; Yang, Zichao; Yao, Xiaotong; Song, Fengbin; Zhang, Runzhi; Wang, Xuerong; Xu, Ning; Zhang, Chunyi; Li, Wei; Li, Shumin

2017-01-01

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving the problems of greenhouse eggplant monocultures. PMID:28346463

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses.

PubMed

Li, Tianzhu; Liu, Tongtong; Zheng, Chengyu; Kang, Chunsheng; Yang, Zichao; Yao, Xiaotong; Song, Fengbin; Zhang, Runzhi; Wang, Xuerong; Xu, Ning; Zhang, Chunyi; Li, Wei; Li, Shumin

2017-01-01

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving the problems of greenhouse eggplant monocultures.

The effects of vegetation and soil hydraulic properties on passive microwave sensing of soil moisture: Data report for the 1982 fiels experiments

NASA Technical Reports Server (NTRS)

Oneill, P.; Jackson, T.; Blanchard, B. J.; Vandenhoek, R.; Gould, W.; Wang, J.; Glazar, W.; Mcmurtrey, J., III

1983-01-01

Field experiments to (1) study the biomass and geometrical structure properties of vegetation canopies to determine their impact on microwave emission data, and (2) to verify whether time series microwave data can be related to soil hydrologic properties for use in soil type classification. Truck mounted radiometers at 1.4 GHz and 5 GHz were used to obtain microwave brightness temperatures of bare vegetated test plots under different conditions of soil wetness, plant water content and canopy structure. Observations of soil moisture, soil temperature, vegetation biomass and other soil and canopy parameters were made concurrently with the microwave measurements. The experimental design and data collection procedures for both experiments are documented and the reduced data are presented in tabular form.

Enhancing soil begins with soil biology and a stable soil microclimate

USDA-ARS?s Scientific Manuscript database

Protection of the soil resource from erosion requires reducing the surface impact from raindrop energy and maintaining soil structure and stability to allow more efficient infiltration of water into the soil column. These two processes are linked with practices associated with enhancing and maintain...

Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil.

PubMed

Deng, Linjing; Zeng, Guangming; Fan, Changzheng; Lu, Lunhui; Chen, Xunfeng; Chen, Ming; Wu, Haipeng; He, Xiaoxiao; He, Yan

2015-10-01

Due to the emerging environmental issues related to heavy metals, concern about the soil quality of farming lands near manufacturing district is increasing. Investigating the function of soil microorganisms exposed to long-term heavy metal contamination is meaningful and important for agricultural soil utilization. This article studied the potential influence of several heavy metals on microbial biomass, activity, abundance, and community composition in arable soil near industrial estate in Zhuzhou, Hunan province, China. The results showed that soil organic contents (SOC) were significantly positive correlated with heavy metals, whereas dehydrogenase activity (DHA) was greatly depressed by the heavy metal stress. Negative correlation was found between heavy metals and basal soil respiration (BSR), and no correlation was found between heavy metals and microbial biomass content (MBC). The quantitative PCR (QPCR) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis could suggest that heavy metal pollution has significantly decreased abundance of bacteria and fungi and also changed their community structure. The results could contribute to evaluate heavy metal pollution level in soil. By combining different environmental parameters, it would promote the better understanding of heavy metal effect on the size, structure, and activity of microbial community in arable soil.

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE PAGES

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe; ...

2014-06-16

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota.

PubMed

Leiva, Diego; Clavero-León, Claudia; Carú, Margarita; Orlando, Julieta

2016-11-01

Definition of lichens has evolved from bi(tri)partite associations to multi-species symbioses, where bacteria would play essential roles. Besides, although soil bacterial communities are known to be affected by edaphic factors, when lichens grow upon them these could become less preponderant. We hypothesized that the structure of both the lichen microbiota and the microbiota in the soil underneath lichens is shaped by lichen intrinsic and extrinsic factors. In this work, intrinsic factors corresponded to mycobiont and cyanobiont identities of Peltigera lichens, metabolite diversity and phenoloxidase activity and extrinsic factors involved the site of the forest where lichens grow. Likewise, the genetic and metabolic structure of the lichen and soil bacterial communities were analyzed by fingerprinting. Among the results, metabolite diversity was inversely related to the genetic structure of bacterial communities of lichens and soils, highlighting the far-reaching effect of these substances; while phenoloxidase activity was inversely related to the metabolic structure only of the lichen bacterial microbiota, presuming a more limited effect of the products of these enzymes. Soil bacterial microbiota was different depending on the site and, strikingly, according to the cyanobiont present in the lichen over them, which could indicate an influence of the photobiont metabolism on the availability of soil nutrients. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Soil phosphorus depletion and shifts in plant communities change bacterial community structure in a long-term grassland management trial.

PubMed

Adair, Karen L; Wratten, Steve; Lear, Gavin

2013-06-01

Agricultural systems rely on healthy soils and their sustainability requires understanding the long-term impacts of agricultural practices on soils, including microbial communities. We examined the impact of 17 years of land management on soil bacterial communities in a New Zealand randomized-block pasture trial. Significant variation in bacterial community structure related to mowing and plant biomass removal, while nitrogen fertilizer had no effect. Changes in soil chemistry and legume abundance described 52% of the observed variation in the bacterial community structure. Legumes (Trifolium species) were absent in unmanaged plots but increased in abundance with management intensity; 11% of the variation in soil bacterial community structure was attributed to this shift in the plant community. Olsen P explained 10% of the observed heterogeneity, which is likely due to persistent biomass removal resulting in P limitation; Olsen P was significantly lower in plots with biomass removed (14 mg kg(-1) ± 1.3SE) compared with plots that were not mown, or where biomass was left after mowing (32 mg kg(-1) ± 1.6SE). Our results suggest that removal of plant biomass and associated phosphorus, as well as shifts in the plant community, have greater long-term impacts on soil bacterial community structure than application of nitrogen fertilizers. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Spatial and seasonal variations in mercury methylation and microbial community structure in a historic mercury mining area, Yolo County, California

USGS Publications Warehouse

Holloway, J.M.; Goldhaber, M.B.; Scow, K.M.; Drenovsky, R.E.

2009-01-01

The relationships between soil parent lithology, nutrient concentrations, microbial biomass and community structure were evaluated in soils from a small watershed impacted by historic Hg mining. Upland and wetland soils, stream sediments and tailings were collected and analyzed for nutrients (DOC, SO4=, NO3-), Hg, MeHg, and phospholipid fatty acids (PLFA). Stream sediment was derived from serpentinite, siltstone, volcanic rocks and mineralized serpentine with cinnabar, metacinnabar and other Hg phases. Soils from different parent materials had distinct PLFA biomass and community structures that are related to nutrient concentrations and toxicity effects of trace metals including Hg. The formation of MeHg appears to be most strongly linked to soil moisture, which in turn has a correlative relationship with PLFA biomass in wetland soils. The greatest concentrations of MeHg (> 0.5??ng g- 1 MeHg) were measured in wetland soils and soil with a volcanic parent (9.5-37????g g- 1 Hg). Mercury methylation was associated with sulfate-reducing bacteria, including Desulfobacter sp. and Desulfovibrio sp., although these organisms are not exclusively responsible for Hg methylation. Statistical models of the data demonstrated that soil microbial communities varied more with soil type than with season.

Increased Electron-Accepting and Decreased Electron-Donating Capacities of Soil Humic Substances in Response to Increasing Temperature.

PubMed

Tan, Wenbing; Xi, Beidou; Wang, Guoan; Jiang, Jie; He, Xiaosong; Mao, Xuhui; Gao, Rutai; Huang, Caihong; Zhang, Hui; Li, Dan; Jia, Yufu; Yuan, Ying; Zhao, Xinyu

2017-03-21

The electron transfer capacities (ETCs) of soil humic substances (HSs) are linked to the type and abundance of redox-active functional moieties in their structure. Natural temperature can affect the chemical structure of natural organic matter by regulating their oxidative transformation and degradation in soil. However, it is unclear if there is a direct correlation between ETC of soil HS and mean annual temperature. In this study, we assess the response of the electron-accepting and -donating capacities (EAC and EDC) of soil HSs to temperature by analyzing HSs extracted from soil set along glacial-interglacial cycles through loess-palaeosol sequences and along natural temperature gradients through latitude and altitude transects. We show that the EAC and EDC of soil HSs increase and decrease, respectively, with increasing temperature. Increased temperature facilitates the prevalence of oxidative degradation and transformation of HS in soils, thus potentially promoting the preferentially oxidative degradation of phenol moieties of HS or the oxidative transformation of electron-donating phenol moieties to electron-accepting quinone moieties in the HS structure. Consequently, the EAC and EDC of HSs in soil increase and decrease, respectively. The results of this study could help to understand biogeochemical processes, wherein the redox functionality of soil organic matter is involved in the context of increasing temperature.

Impact of monovalent cations on soil structure. Part II. Results of two Swiss soils

NASA Astrophysics Data System (ADS)

Farahani, Elham; Emami, Hojat; Keller, Thomas

2018-01-01

In this study, we investigated the impact of adding solutions with different potassium and sodium concentrations on dispersible clay, water retention characteristics, air permeability, and soil shrinkage behaviour using two agricultural soils from Switzerland with different clay content but similar organic carbon to clay ratio. Three different solutions (including only Na, only K, and the combination of both) were added to soil samples at three different cation ratio of soil structural stability levels, and the soil samples were incubated for one month. Our findings showed that the amount of readily dispersible clay increased with increasing Na concentrations and with increasing cation ratio of soil structural stability. The treatment with the maximum Na concentration resulted in the highest water retention and in the lowest shrinkage capacity. This was was associated with high amounts of readily dispersible clay. Air permeability generally increased during incubation due to moderate wetting and drying cycles, but the increase was negatively correlated with readily dispersible clay. Readily dispersible clay decreased with increasing K, while readily dispersible clay increased with increasing K in Iranian soil (Part I of our study). This can be attributed to the different clay mineralogy of the studied soils (muscovite in Part I and illite in Part II).

Modelling and interpreting biologically crusted dryland soil sub-surface structure using automated micropenetrometry

NASA Astrophysics Data System (ADS)

Hoon, Stephen R.; Felde, Vincent J. M. N. L.; Drahorad, Sylvie L.; Felix-Henningsen, Peter

2015-04-01

Soil penetrometers are used routinely to determine the shear strength of soils and deformable sediments both at the surface and throughout a depth profile in disciplines as diverse as soil science, agriculture, geoengineering and alpine avalanche-safety (e.g. Grunwald et al. 2001, Van Herwijnen et al. 2009). Generically, penetrometers comprise two principal components: An advancing probe, and a transducer; the latter to measure the pressure or force required to cause the probe to penetrate or advance through the soil or sediment. The force transducer employed to determine the pressure can range, for example, from a simple mechanical spring gauge to an automatically data-logged electronic transducer. Automated computer control of the penetrometer step size and probe advance rate enables precise measurements to be made down to a resolution of 10's of microns, (e.g. the automated electronic micropenetrometer (EMP) described by Drahorad 2012). Here we discuss the determination, modelling and interpretation of biologically crusted dryland soil sub-surface structures using automated micropenetrometry. We outline a model enabling the interpretation of depth dependent penetration resistance (PR) profiles and their spatial differentials using the model equations, σ {}(z) ={}σ c0{}+Σ 1n[σ n{}(z){}+anz + bnz2] and dσ /dz = Σ 1n[dσ n(z) /dz{} {}+{}Frn(z)] where σ c0 and σ n are the plastic deformation stresses for the surface and nth soil structure (e.g. soil crust, layer, horizon or void) respectively, and Frn(z)dz is the frictional work done per unit volume by sliding the penetrometer rod an incremental distance, dz, through the nth layer. Both σ n(z) and Frn(z) are related to soil structure. They determine the form of σ {}(z){} measured by the EMP transducer. The model enables pores (regions of zero deformation stress) to be distinguished from changes in layer structure or probe friction. We have applied this method to both artificial calibration soils in the laboratory, and in-situ field studies. In particular, we discuss the nature and detection of surface and buried (fossil) subsurface Biological Soil Crusts (BSCs), voids, macroscopic particles and compositional layers. The strength of surface BSCs and the occurrence of buried BSCs and layers has been detected at sub millimetre scales to depths of 40mm. Our measurements and field observations of PR show the importance of morphological layering to overall BSC functions (Felde et al. 2015). We also discuss the effect of penetrometer shaft and probe-tip profiles upon the theoretical and experimental curves, EMP resolution and reproducibility, demonstrating how the model enables voids, buried biological soil crusts, exotic particles, soil horizons and layers to be distinguished one from another. This represents a potentially important contribution to advancing understanding of the relationship between BSCs and dryland soil structure. References: Drahorad SL, Felix-Henningsen P. (2012) An electronic micropenetrometer (EMP) for field measurements of biological soil crust stability, J. Plant Nutr. Soil Sci., 175, 519-520 Felde V.J.M.N.L., Drahorad S.L., Felix-Henningsen P., Hoon S.R. (2015) Ongoing oversanding induces biological soil crust layering - a new approach for BSC structure elucidation determined from high resolution penetration resistance data (submitted) Grunwald, S., Rooney D.J., McSweeney K., Lowery B. (2001) Development of pedotransfer functions for a profile cone penetrometer, Geoderma, 100, 25-47 Van Herwijnen A., Bellaire S., Schweizer J. (2009) Comparison of micro-structural snowpack parameters derived from penetration resistance measurements with fracture character observations from compression tests, Cold Regions Sci. {& Technol.}, 59, 193-201

Responses of redwood soil microbial community structure and N transformations to climate change

Treesearch

Damon C. Bradbury; Mary K. Firestone

2012-01-01

Soil microorganisms perform critical ecosystem functions, including decomposition, nitrogen (N) mineralization and nitrification. Soil temperature and water availability can be critical determinants of the rates of these processes as well as microbial community composition and structure. This research examined how changes in climate affect bacterial and fungal...

Single application of Sewage Sludge to an Alluvial Agricultural Soil - impacts on Soil Quality

NASA Astrophysics Data System (ADS)

Suhadolc, M.; Graham, D. B.; Hagn, A.; Doerfler, U.; Schloter, M.; Schroll, R.; Munch, J. C.; Lobnik, F.

2009-04-01

Limited information exists on the effects of sewage sludge on soil quality with regard to their ability to maintain soil functions. We studied effects of sewage sludge amendment on soil chemical properties, microbial community structure and microbial degradation of the herbicide glyphosate. Three months soil column leaching experiment has been conducted using alluvial soils (Eutric Fluvisol) with no prior history of sludge application. The soil was loamy with pH 7,4 and organic matter content of 3,5%. Soil material in the upper 2 cm of columns was mixed with dehydrated sewage sludge which was applied in amounts corresponding to the standards governing the use of sewage sludge for agricultural land. Sludge did increase some nutrients (total N, NH4+, available P and K, organic carbon) and some heavy metals contents (Zn, Cu, Pb) in soil. However, upper limits for heavy metals in agricultural soils were not exceeded. Results of heavy metal availability in soil determined by sequential extraction will be also presented. Restriction fragment length polymorphism (RFLP) analyses of 16s/18s rDNA, using universal fungal and bacterial primers, revealed clear shifts in bacterial and fungal community structure in the upper 2 cm of soils after amendment. Fungal fingerprints showed greater short term effects of sewage sludge, whereas sewage sludge seems to have prolonged effects on soil bacteria. Furthermore, sewage sludge amendment significantly increased glyphosate degradation from 21.6±1% to 33.6±1% over a 2 months period. The most probable reasons for shifts in microbial community structure and increased degradation of glyphosate are beneficial alterations to the physical-chemical characteristics of the soil. Negative effects of potentially toxic substances present in the sewage sludge on soil microbial community functioning were not observed with the methods used in our study.

Conceptional Considerations to Energy Balance and Global Warming Potential of Soil Bioengineering Structures

NASA Astrophysics Data System (ADS)

von der Thannen, Magdalena; Paratscha, Roman; Smutny, Roman; Lampalzer, Thomas; Strauss, Alfred; Rauch, Hans Peter

2016-04-01

Nowadays there is a high demand on engineering solutions considering not only technical aspects but also ecological and aesthetic values. In this context soil bioengineering techniques are often used as standalone solutions or in combination with conventional engineering structures. It is a construction technique that uses biological components for hydraulic and civil engineering solutions. In general it pursues the same objectives as conventional civil engineering structures. Currently the used assessment methods for soil bioengineering structures are referencing technically, ecologically and socio-economically. In a modern engineering approach additionally, environmental impacts and potential added values should be considered. The research project E-Protect aims at developing Environmental Life Cycle Assessment (LCA) models for this special field of alpine protective constructions. Both, the Cumulative Energy Demand (CED) and the Global Warming Potential (GWP) should be considered in an Environmental LCA over the whole life cycle of an engineering structure. The life cycle itself can be divided into three phases: the construction phase, the use phase and the end of life phase. The paper represents a concept to apply an Environmental LCA model for soil bioengineering structures. Beside the construction phase of these structures particular attention will be given to the use phase. It is not only important in terms of engineering effects but also plays an important role for positive carbon footprint due to the growing plants of soil bioengineering structures in contrast to conventional structures. Innovative Environmental LCA models will be applied to soil bioengineering structures which provide a new transparency for the responsible planners and stakeholders, by pointing out the total consumption of resources in all construction phases and components.

Rhizosphere biophysics and root water uptake

NASA Astrophysics Data System (ADS)

Carminati, Andrea; Zarebanadkouki, Mohsen; Ahmed, Mutez A.; Passioura, John

2016-04-01

The flow of water into the roots and the (putative) presence of a large resistance at the root-soil interface have attracted the attention of plant and soil scientists for decades. Such resistance has been attributed to a partial contact between roots and soil, large gradients in soil matric potential around the roots, or accumulation of solutes at the root surface creating a negative osmotic potential. Our hypothesis is that roots are capable of altering the biophysical properties of the soil around the roots, the rhizosphere, facilitating root water uptake in dry soils. In particular, we expect that root hairs and mucilage optimally connect the roots to the soil maintaining the hydraulic continuity across the rhizosphere. Using a pressure chamber apparatus we measured the relation between transpiration rate and the water potential difference between soil and leaf xylem during drying cycles in barley mutants with and without root hairs. The samples were grown in well structured soils. At low soil moistures and high transpiration rates, large drops in water potential developed around the roots. These drops in water potential recovered very slowly, even after transpiration was severely decreased. The drops in water potential were much bigger in barley mutants without root hairs. These mutants failed to sustain high transpiration rates in dry conditions. To explain the nature of such drops in water potential across the rhizosphere we performed high resolution neutron tomography of the rhizosphere of the barleys with and without root hairs growing in the same soil described above. The tomograms suggested that the hydraulic contact between the soil structures was the highest resistance for the water flow in dry conditions. The tomograms also indicate that root hairs and mucilage improved the hydraulic contact between roots and soil structures. At high transpiration rates and low water contents, roots extracted water from the rhizosphere, while the bulk soil, due its low unsaturated conductivity, failed to compensate root water uptake. We conclude that root hairs are functional to increase the contact area between the roots and the soil structures and mucilage maintains wet the soil region between root hairs. These observations demonstrate the importance of the biophysical processes in the rhizosphere in modulating root water uptake.

Land use and hydromechanical heterogeneities in marshland soils.

NASA Astrophysics Data System (ADS)

Tojo Radimy, Raymond; Dupont, Jean-Paul; Dudoignon, Patrick

2017-04-01

In the interpretation of soil moisture profiles, mechanical properties were most often considered homogeneous. The structural heterogeneities of the soil are knows to be at the origin of the distribution and the availability of water in the vadose zone. The soils study is located in the French Atlantic coastal marshlands, characterized by the succession polderization/desiccation/consolidation and maturation. The work is carried out within the framework of the farming of old salt marshes with two concerns in the farmers: the salinity of the soil and the distribution of the available water capacity of the soils according to the crop growth. The present work shows the knowledge of the soil storage transfers during seasonal cycles on drained corn field and undrained grassland. We analyze the vertical water profiles observed to reveal the hydromechanical heterogeneities in the soils depending the porosity and gravity water parameter. This approach is based on mechanical tests between the compaction pathways carried out in the laboratory using materials taken in situ. Comparing to grasslands profiles, we highlight the influence of agricultural practices and the establishment of drainage in the marshland. However, the vertical homogenization of hydromechanical structures, desalination has been taken into account for the estimation of water in crop. The concept of a homogeneous structure is not adapted to real vertical profile. Finally, the authors conclude by discussing the notion of the mechanical availability of water in terms of porosity and gravity water. These parameters are good tools to the sustainable management of marshland soils. Keywords: hydromechanics, vadose zone, soil structure, land use, available water capacity

Environmental Factors Shaping the Community Structure of Ammonia-Oxidizing Bacteria and Archaea in Sugarcane Field Soil

PubMed Central

Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

2015-01-01

The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers’ fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers’ sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 105–9.2 × 106 and 1.7 × 106–5.3 × 107 gene copies g dry soil−1, respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields. PMID:25736866

Effects of imidacloprid on soil microbial communities in different saline soils.

PubMed

Zhang, Qingming; Xue, Changhui; Wang, Caixia

2015-12-01

The effects of imidacloprid in the soil environment are a worldwide concern. However, the impact of imidacloprid on soil microorganisms under salt stress is almost unknown. Therefore, an indoor incubation test was performed, and the denaturing gradient gel electrophoresis (DGGE) approach was used to determine the response of different saline soil bacterial and fungal community structures to the presence of imidacloprid (0.4, 2, 10 mg kg(-1)). The results showed that the soil bacterial diversity slightly declined with increasing imidacloprid concentration in soils with low salinity. In moderately saline soils, a new band in the DGGE profile suggested that imidacloprid could improve the soil bacterial diversity to some degree. An analysis of variance indicated that the measured soil bacterial diversity parameters were significantly affected by dose and incubation time. Compared with the control, the soil fungal community structure showed no obvious changes in low and moderately saline soils treated with imidacloprid. The results of these observations provide a basic understanding of the potential ecological effects of imidacloprid on different microorganisms in saline soils.

Bacterial phylogeny structures soil resistomes across habitats

PubMed Central

Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

2014-01-01

Summary Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil1–3, including genes identical to those in human pathogens4. Despite the apparent overlap between soil and clinical resistomes4–6, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown3. General metagenome functions often correlate with the underlying structure of bacterial communities7–12. However, ARGs are hypothesized to be highly mobile4,5,13, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions13,14. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2895 ARGs we discovered were predominantly novel, and represent all major resistance mechanisms15. We demonstrate that distinct soil types harbor distinct resistomes, and that nitrogen fertilizer amendments strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements syntenic with ARGs were rare in soil compared to sequenced pathogens, suggesting that ARGs in the soil may not transfer between bacteria as readily as is observed in the clinic. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny13,14. PMID:24847883

Bacterial phylogeny structures soil resistomes across habitats

NASA Astrophysics Data System (ADS)

Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

2014-05-01

Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.

[Effect of ground mulch managements on soil bacterial community structure and diversity in the non-irrigated apple orchard in Weibei Loess Plateau].

PubMed

Chen, Yuexing; Wen, Xiaoxia; Sun, Yulin; Zhang, Junli; Lin, Xiaoli; Liao, Yuncheng

2015-07-04

We studied the changes in soil bacterial communities induced by ground mulch managements at different apple growth periods. We adopted the denaturing gradient gel electrophoresis (DGGE) with PCR-amplified 16S rRNA fragments to determine soil bacterial community structure and diversity. Soil bacterial community structure with different ground mulch managements were significantly different. Both the mulch management strategies and apple growth periods affected the predominant groups and their abundance in soil bacterial communities. Grass mulch and cornstalk mulch treatments had higher bacterial diversity and richness than the control at young fruit period and fruit expanding period, whereas film mulch treatment had no significant difference compared with the control. During mature period, bacterial diversity in the control reached its maximum, which may be ascribed to the rapid growth and reproduction of the r-selection bacteria. The clustering and detrended correspondence analysis revealed that differences in soil bacterial communities were closely correlated to apple growth periods and ground mulch managements. Soil samples from the grass mulch and cornstalk mulch treatments clustered together while those mulched with plastic film treatment were similar to the control. The most abundant phylum in soil bacterial community was Proteobacteria followed by Bacteroidetes. Some other phyla were also detected, such as Acidobacteria, Firmicutes, Actinobacteria and Chloroflexi. Mulching with plant (Grass/Cornstalk) had great effects on soil bacterial community structure and enhanced the diversity while film mulch management had no significant effects.

Effects of soil structure destruction on methane production and carbon partitioning between methanogenic pathways in tropical rain forest soils

NASA Astrophysics Data System (ADS)

Teh, Yit Arn; Silver, Whendee L.

2006-03-01

Controls on methanogenesis are often determined from laboratory incubations of soils converted to slurries. Destruction of soil structure during slurry conversion may disrupt syntrophic associations, kill methanogens, and/or alter the microsite distribution of methanogenic activity, suppressing CH4 production. The effects of slurry conversion on methanogenesis were investigated to determine if disruption of aggregate structure impacted methanogenesis, substrate utilization, and C partitioning between methanogenic pathways. Soils were collected from the tropical rain forest life zone of the Luquillo Experimental Forest, Puerto Rico, and exposed to different physical disturbances, including flooding and physical homogenization. Slurry conversion negatively impacted methanogenesis. Rates of CH4 production declined by a factor of 17 after well-aggregated soils were converted to slurries. Significantly more 13C-acetate was recovered in CO2 compared to CH4 after slurry conversion, suggesting that methanogens consumed less acetate after slurry conversion and may have competed less effectively with other anaerobes for acetate. Isotopic data indicate that the relative partitioning of C between aceticlastic and hydrogenotrophic pathways was unchanged after slurry conversion. These data suggest that experiments which destroy soil structure may significantly underestimate methanogenesis and overestimate the potential for other microorganisms to compete with methanogens for organic substrates. Current knowledge of the factors that regulate methanogenesis in soil may be biased by the findings of slurry-based experiments, that do not accurately represent the complex, spatially heterogeneous conditions found in well-aggregated soils.

Relationship between chemical structure of soil organic matter and intra-aggregate pore structure: evidence from X-ray computed micro-tomography

NASA Astrophysics Data System (ADS)

Kravchenko, Alexandra; Grandy, Stuart A.

2014-05-01

Understanding chemical structure of soil organic matter (SOM) and factors that affect it are vital for gaining understanding of mechanisms of C sequestration by soil. Physical protection of C by adsorption to mineral particles and physical disconnection between C sources and microbial decomposers is now regarded as the key component of soil C sequestration. Both of the processes are greatly influenced by micro-scale structure and distribution of soil pores. However, because SOM chemical structure is typically studied in disturbed (ground and sieved) soil samples the experimental evidence of the relationships between soil pore structure and chemical structure of SOM are still scarce. Our study takes advantage of the X-ray computed micro-tomography (µ-CT) tools that enable non-destructive analysis of pore structure in intact soil samples. The objective of this study is to examine the relationship between SOM chemical structure and pore-characteristics in intact soil macro-aggregates from two contrasting long-term land uses. The two studied land use treatments are a conventionally tilled corn-soybean-wheat rotation treatment and a native succession vegetation treatment removed from agricultural use >20 years ago. The study is located in southwest Michigan, USA, on sandy-loam Typic Hapludalfs. For this study we used soil macro-aggregates 4-6 mm in size collected at 0-15 cm depth. The aggregate size was selected so as both to enable high resolution of µ-CT and to provide sufficient amount of soil for C measurements. X-ray µ-CT scanning was conducted at APS Argonne at a scanning resolution of 14 µm. Two scanned aggregates (1 per treatment) were used in this preliminary study. Each aggregate was cut into 7 "geo-referenced" sections. Analyses of pore characteristics in each section were conducted using 3DMA and ImageJ image analysis tools. SOM chemistry was analyzed using pyrolysis/gas chromatography-mass spectroscopy. Results demonstrated that the relationships between SOM chemical structure and pore characteristics differed in the aggregates of the two treatments. For example, in the agricultural treatment, the aggregate sections with prevalence of small pores had lower relative lignin abundance, while higher lignin abundances occurred in aggregate sections with more large pores. This relationship could be reflecting the low accessibility of the sections dominated by small pores to plant roots. It is interesting to note that no relationship between pores and lignin were observed in the aggregate from the native succession treatment. In the native succession aggregate we found that a larger presence of protein and N-bearing compounds was associated with sections with greater presence of 35-90 µm pores. This could be a result of fungal activities, as pores of this size constitute a primary fungal habitat and fungi are known for secreting proteins. Fewer fungi in the soil under agricultural management are likely the reason that no such relationship was observed in the aggregate from the agricultural treatment. Our preliminary results indicate that substantial spatial variability patterns in SOM chemical structure can exist even within a single macro-aggregate and that pores are likely a main driver of intra-aggregate SOM chemistry.

Soil and substrate morphology as witnesses of present and former agricultural landscape management

NASA Astrophysics Data System (ADS)

Chartin, C.; Salvador-Blanes, S.; Hinschberger, F.; Bourennane, H.; Macaire, J.-J.

2009-04-01

Water and tillage erosion, combined with the effect of successive regrouping of the land campaigns, have sensibly modified the morphology of cultivated hillslopes. Nowadays, we can still observe over cultivated landscapes various anthropogenic structures (e.g. lynchets) that correspond to former and/or present field limits. The aim of this work is to spatially characterise the geometry of these various structures, and to assess their relation with soil variability. The 10 ha studied site corresponds to an hillslope located in a small calcareous watershed near Tours in the Parisian Basin (France). Soils are mainly Cambisols (calcaric), Epileptic cambisols (calcaric) and Colluvic cambisols. This watershed is characterised by the presence of many soil accumulation structures and has been submitted to an important regrouping of the lands since the 1960's. The existing structures were accurately located and defined through a topographical analysis (slope, profile curvature...), and then related to past and present field limits using aerial photographies and cadastral maps. Two main morphological structures, deeply marked in the topography, are identified. The most remarkable type corresponds to well developed lynchets located at the lower part of field limits. Secondary structures, less marked than lynchets, are linked to field limits which existed at least since 1836, but that disappeared from the 1960's. These secondary structures look like longitudinal bulges placed perpendicularly to the direction of the main slope. A soil survey on these two geomorphic structure types has been performed in order to determine their specific geometry. Lynchets are characterised by a large increase in the thickness of soils: from 35 cm at 24 m upslope to more than 120 cm on its top. But, in some cases, the elevation study shows a topographical discontinuity between the top of the accumulation and the field or road below, discontinuity that is more important than the maximum soil thickness observed in the lynchet. This implies that the substrate, which is mostly homogeneous, has been largely excavated below these limits certainly due to repeated tillage operations. Concerning the secondary structures, soil thickness increases slightly from 35 cm at 16 m up- and downslope the former field limit to 70 cm at the maximum of the bulges convexity. However, the slope morphology seems to show larger soil accumulation considering a regular substrate morphology along the hillslope profile. Here too, by combining soil thickness and surface topography, we show that the substrate has certainly been strongly remodelled at these former field limits by tillage erosion. The spatial variability of the various soils types is closely linked to the sequence of structures oriented perpendicularly to the direction of the main slope. Although the current topography is clearly marked by various structures linked to former and present field limits, it appears that soil thickness is not the only factor explaining these large variations in the slope morphology: long-term agricultural practices, certainly tillage, "shape" the substrate as well. It is thus important to take into account these substrate excavations for sediment budget studies. The use of tracers such as 137Cs will allow to understand the intensity of these morphological changes at the slope scale within the last decades.

Changes in microbial structure and functional communities at different soil depths during 13C labelled root litter degradation

NASA Astrophysics Data System (ADS)

Sanaullah, Muhammad; Baumann, Karen; Chabbi, Abad; Dignac, Marie-France; Maron, Pierre-Alain; Kuzyakov, Yakov; Rumpel, Cornelia

2014-05-01

Soil organic matter turnover depends on substrate quality and microbial activity in soil but little is known about how addition of freshly added organic material modifies the diversity of soil microbial communities with in a soil profile. We took advantage of a decomposition experiment, which was carried out at different soil depths under field conditions and sampled litterbags with 13C-labelled wheat roots, incubated in subsoil horizons at 30, 60 and 90 cm depth for up to 36 months. The effect of root litter addition on microbial community structure, diversity and activity was studied by determining total microbial biomass, PLFA signatures, molecular tools (DNA genotyping and pyrosequencing of 16S and 18S rDNAs) and extracellular enzyme activities. Automated ribosomal intergenic spacer analysis (ARISA) was also carried out to determine the differences in microbial community structure. We found that with the addition of root litter, total microbial biomass as well as microbial community composition and structure changed at different soil depths and change was significantly higher at top 30cm soil layer. Moreover, in the topsoil, population of both gram-positive and gram-negative bacteria increased with root litter addition over time, while subsoil horizons were relatively dominated by fungal community. Extra-cellular enzyme activities confirmed relatively higher fungal community at subsoil horizons compared with surface soil layer with bacteria dominant microbial population. Bacterial-ARISA profiling illustrated that the addition of root litter enhanced the abundance of Actinobacteria and Proteobacteria, at all three soil depths. These bacteria correspond to copiotrophic attributes, which can preferentially consume of labile soil organic C pools. While disappearance of oligotrophic Acidobacteria confirmed the shifting of microbial communities due to the addition of readily available substrate. We concluded that root litter mixing altered microbial community development which was soil horizon specific and its effects on soil microbial activity may impact on nutrient cycling.

Using the Subsurface Soil Sounding Radar for Investigating the Structure and Total Electron Content of the Martian Ionosphere

NASA Astrophysics Data System (ADS)

Smirnov, V. M.; Yushkova, O. V.; Marchuk, V. N.

2018-05-01

The possibilities of using the Martian soil subsurface sounding radar for investigating the structure of the plasma shell surrounding the planet have been considered. Based on the numerical modeling results and actual soil sounding data, it has been shown that the soil sounding mode of the radio-locating MARSIS radar can be used to assess the structure of the Martian ionosphere. As the emitted signals pass to the planet's surface, it is possible to use the reflected signals to estimate the total electron content of the Martian ionosphere along the flight track of the spacecraft.

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing.

PubMed

Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

2015-01-01

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system.

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing

PubMed Central

Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

2015-01-01

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system. PMID:26317364

Soil bacterial communities are shaped by temporal and environmental filtering: evidence from a long-term chronosequence.

PubMed

Freedman, Zachary; Zak, Donald R

2015-09-01

Soil microbial communities are abundant, hyper-diverse and mediate global biogeochemical cycles, but we do not yet understand the processes mediating their assembly. Current hypothetical frameworks suggest temporal (e.g. dispersal limitation) and environmental (e.g. soil pH) filters shape microbial community composition; however, there is limited empirical evidence supporting this framework in the hyper-diverse soil environment, particularly at large spatial (i.e. regional to continental) and temporal (i.e. 100 to 1000 years) scales. Here, we present evidence from a long-term chronosequence (4000 years) that temporal and environmental filters do indeed shape soil bacterial community composition. Furthermore, nearly 20 years of environmental monitoring allowed us to control for potentially confounding environmental variation. Soil bacterial communities were phylogenetically distinct across the chronosequence. We determined that temporal and environmental factors accounted for significant portions of bacterial phylogenetic structure using distance-based linear models. Environmental factors together accounted for the majority of phylogenetic structure, namely, soil temperature (19%), pH (17%) and litter carbon:nitrogen (C:N; 17%). However, of all individual factors, time since deglaciation accounted for the greatest proportion of bacterial phylogenetic structure (20%). Taken together, our results provide empirical evidence that temporal and environmental filters act together to structure soil bacterial communities across large spatial and long-term temporal scales. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Impact of soil structure heterogeneity on the degradation of organic pollutants at the centimeter scale : 3D Modeling using graph based method

NASA Astrophysics Data System (ADS)

Sinclair Yemini, Francis; Chenu, Claire; Monga, Olivier; Vieuble Gonond, Laure; Juarez, Sabrina; Pihneiro, Marc; otten, Wilfred; Garnier, Patricia

2014-05-01

Contaminant degradation by microorganisms is very variable in soils because of the very heterogeneous spatial relationship of contaminant/degraders. Repacked Soil columns were carried out to study the degradation of 2,4D pesticide labelled with C14 for different scenarios of microorganisms and pesticide initial location. Measurements of global C14-CO2 emission and C14 distribution in the soil column showed that the initial location play a crucial rule on the dissipation of the pollutant. Experiments were simulated using a 3D model able to model microbial degradation and substrate diffusion between aggregates by considering explicitly the 3D structure of soil from CT images. The initial version of the model (Monga et al., 2008) was improved in order to simulate diffusion in samples of large size. Partial differential equations were implemented using freefem++ solver. The model simulates properly the dynamics of 2,4D in the column for the different initial situations. CT images of the same soil but using undisturbed structure instead of repacked aggregates were also carried out. Significant differences of the simulated results were observed between the repacked and the undisturbed soil. The conclusion of our work is that the heterogeneity of the soil structure and location of pollutants and decomposers has a very strong influence on the dissipation of pollutants.

Soil mixing design methods and construction techniques for use in high organic soils.

DOT National Transportation Integrated Search

2015-06-01

Organic soils present a difficult challenge for roadway designers and construction due to the high : compressibility of the soil structure and the often associated high water table and moisture content. For : other soft or loose inorganic soils, stab...

Pyrosequencing of microbial community of typical chernozem in contrast land use conditions

NASA Astrophysics Data System (ADS)

Ivanova, Ekaterina; Olga, Kutovaya; Azida, Tkhakakhova

2015-04-01

Chernozems are the principal soil resourse of Russia, so the sustainable use of these fertile soils in the intensive agriculturural production is of great importance, especially in terms of agro-ecological security of the country. The increase in agricultural inputs - intensive cropping, soil fallowing application accompanied with high frequency of mechanical treatment, result in decrease in soil organic matter content as well as soil structure degradation and, finally, lead to the loss of soil fertility. Soil microorganisms can serve as bioindicators of anthropogenic stress experienced by the soil during its agricultural use, so they may be universal indicators of soil quality (soil health) used for optimization and biologization of agricultural systems. The way to study the relationship between the structural status of the soil, its microbial communities and the organic matter content is the comparative analysis of soil aggregates in conditions of different land use practices. The objects of our research were soil samples of soil with permanent wheat cropping (50 years), continuous dead fallow (50 years) soil, and recovering soil (for 18 years under native steppe vegetation, fallowed in previous). The analysis of 16 S rRNA gene amplicon libraries of typical chernozem in conditions of different land use systems revealed that the way of agricultural use is a strong determinant of soil microbiome taxonomic composition. It was shown that the continuous «dead fallowing» application (for 50 years) lead to the establishment of olygothrophic components of microbial community, including spore-forming members of phylum Firmicutes. The increase of Acidobacteria lineages in this variant may be an indicator of some acidification of soil during long-time fallowing application. The variant of continuous wheat cropping lead to increasing in Proteobacteria lineages. The variant of soil under native steppe vegetation was characterized by the highest values of biodiversity indices - species richness and eveness, which can indicate the occurrence of soil recovering. This variant was also characterized by the maximum content of agricultural valuable aggregate fraction of 2-5 mm size. In soil samples from different aggregate fractions the presence of accessory components was revealed. It was determined that Actinobacteria lineages preferred microaggregates (less than 0.25 mm) rather than coarse aggregate fractions (more than 7 mm). The opposite trend was determined for Proteobacteria: the amount was maximum in aggregates more than 7 mm in diameter. The occurrence of specific components in the taxonomic structure of micro-and macro-aggregates may indicate the presence of a certain size fraction in the structure of the investigated soil. The study of soils' metagenome is promising for the development of both soil microbiology, and for the soil processes trends in soils of anthropogenic origin. The study was supported by Russian Scientific Fund (14-26-00079 and 14-26-00094)

Basin-wide variations in Amazon forest structure and function are mediated by both soils and climate

NASA Astrophysics Data System (ADS)

Quesada, C. A.; Phillips, O. L.; Schwarz, M.; Czimczik, C. I.; Baker, T. R.; Patiño, S.; Fyllas, N. M.; Hodnett, M. G.; Herrera, R.; Almeida, S.; Alvarez Dávila, E.; Arneth, A.; Arroyo, L.; Chao, K. J.; Dezzeo, N.; Erwin, T.; di Fiore, A.; Higuchi, N.; Honorio Coronado, E.; Jimenez, E. M.; Killeen, T.; Lezama, A. T.; Lloyd, G.; López-González, G.; Luizão, F. J.; Malhi, Y.; Monteagudo, A.; Neill, D. A.; Núñez Vargas, P.; Paiva, R.; Peacock, J.; Peñuela, M. C.; Peña Cruz, A.; Pitman, N.; Priante Filho, N.; Prieto, A.; Ramírez, H.; Rudas, A.; Salomão, R.; Santos, A. J. B.; Schmerler, J.; Silva, N.; Silveira, M.; Vásquez, R.; Vieira, I.; Terborgh, J.; Lloyd, J.

2012-06-01

Forest structure and dynamics vary across the Amazon Basin in an east-west gradient coincident with variations in soil fertility and geology. This has resulted in the hypothesis that soil fertility may play an important role in explaining Basin-wide variations in forest biomass, growth and stem turnover rates. Soil samples were collected in a total of 59 different forest plots across the Amazon Basin and analysed for exchangeable cations, carbon, nitrogen and pH, with several phosphorus fractions of likely different plant availability also quantified. Physical properties were additionally examined and an index of soil physical quality developed. Bivariate relationships of soil and climatic properties with above-ground wood productivity, stand-level tree turnover rates, above-ground wood biomass and wood density were first examined with multivariate regression models then applied. Both forms of analysis were undertaken with and without considerations regarding the underlying spatial structure of the dataset. Despite the presence of autocorrelated spatial structures complicating many analyses, forest structure and dynamics were found to be strongly and quantitatively related to edaphic as well as climatic conditions. Basin-wide differences in stand-level turnover rates are mostly influenced by soil physical properties with variations in rates of coarse wood production mostly related to soil phosphorus status. Total soil P was a better predictor of wood production rates than any of the fractionated organic- or inorganic-P pools. This suggests that it is not only the immediately available P forms, but probably the entire soil phosphorus pool that is interacting with forest growth on longer timescales. A role for soil potassium in modulating Amazon forest dynamics through its effects on stand-level wood density was also detected. Taking this into account, otherwise enigmatic variations in stand-level biomass across the Basin were then accounted for through the interacting effects of soil physical and chemical properties with climate. A hypothesis of self-maintaining forest dynamic feedback mechanisms initiated by edaphic conditions is proposed. It is further suggested that this is a major factor determining endogenous disturbance levels, species composition, and forest productivity across the Amazon Basin.

Structural composition of organic matter in particle-size fractions of soils along a climo-biosequence in the main range of Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Jafarzadeh-Haghighi, Amir Hossein; Shamshuddin, Jusop; Hamdan, Jol; Zainuddin, Norhazlin

2016-09-01

Information on structural composition of organic matter (OM) in particle-size fractions of soils along a climo-biosequence is sparse. The objective of this study was to examine structural composition and morphological characteristics of OM in particle-size fractions of soils along a climo-biosequence in order to better understand the factors and processes affecting structural composition of soil organic matter. To explore changes in structural composition of OM in soils with different pedogenesis, the A-horizon was considered for further analyses including particle-size fractionation, solid-state 13C nuclear magnetic resonance (NMR) spectroscopy and scanning electron microscopy (SEM). Due to the increase in the thickness of organic layer with increasing elevation, the A-horizon was situated at greater depth in soils of higher elevation. The relationship between relative abundances of carbon (C) structures and particle-size fractions was examined using principal component analysis (PCA). It was found that alkyl C (20.1-73.4%) and O-alkyl C (16.8-67.7%) dominated particle-size fractions. The proportion of alkyl C increased with increasing elevation, while O-alkyl C showed an opposite trend. Results of PCA confirmed this finding and showed the relative enrichment of alkyl C in soils of higher elevation. Increase in the proportion of alkyl C in 250-2000 μm fraction is linked to selective preservation of aliphatic compounds derived from root litter. SEM results showed an increase in root contribution to the 250-2000 μm fraction with increasing elevation. For the <53 μm fraction, pedogenic process of podzolization is responsible for the relative enrichment of alkyl C. This study demonstrates that changes in structural composition of OM in particle-size fractions of soils along the studied climo-biosequence are attributed to site-specific differences in pedogenesis as a function of climate and vegetation.

Transport of four pharmaceuticals in different horizons of three soil types

NASA Astrophysics Data System (ADS)

Kodesova, Radka; Svatkova, Paula; Klement, Ales; Jaksik, Ondrej; Golovko, Oksana; Fer, Miroslav; Kocarek, Martin; Nikodem, Antonin; Grabic, Roman

2015-04-01

Soil structure, which varies in different soil types and the horizons of these soil types, has a significant impact on water flow and contaminant transport in soils. Transport of many contaminants is in addition strongly influenced by their sorption on soil particles. Transport of four pharmaceuticals (sulfamethoxazole, trimethoprim, atenolol and carbamazepine) was studied in soil columns (a diameter of 10.5 cm and a height of 13 cm) taken from all diagnostic horizons of three different soil types (Haplic Luvisol, Greyic Phaeozem and Haplic Cambisol). The irrigation by water contaminated by a mixture of all four compounds followed by ponding infiltration of distilled water was simulated and water outflow and solute concentrations from the bottom of the soil sample was monitored in time. The highest infiltration rates were observed for soil samples from the Bt horizons of the Greyic Phaeozem that exhibited prismatic structure, followed by rates observed in the Ap horizons of the Haplic Luvisol, Greyic Phaeozem and Haplic Cambisol (due to their granular soil structure and presence of root channels). The lowest infiltration rate was measured for the Bw horizon of the Haplic Cambisol, which had a poorly developed soil structure and a low fraction of macropores. Compound discharge was however also highly affected by their sorption on solids. The highest mobility was observed for sulfamethoxazole followed by carbamazepine atenolol and trimethoprim, which corresponds to measured sorption isotherms. Mobility of ionizable compounds in different soil samples was influenced by pH (i.e. degree and form of their ionization) and sites available for absorption. Mobility of sulfamethoxazole decreased with decreasing pH (i.e. the largest sorption measured in horizons of the Haplic Cambisol). While mobility of atenolol and trimethoprim decreased with increasing base cation saturation, and with increasing organic matter content for carbamazepine. As result of both affects (i.e. soil structure and compounds' sorption) the highest discharge of all compounds was observed from the Ap horizon of the Greyic Phaeozem followed by compound discharge from the C horizons of the Greyic Phaeozem and the C and Bt2 horizons of the Haplic Luvisol. Acknowledgement: The authors acknowledge the financial support of the Czech Science Foundation (Project No. 13-12477S, Transport of pharmaceuticals in soils). References: Kodesova, R., Grabic, R., Kocarek, M., Klement, A., Golovko, O., Fer, M., Nikodem, A., Jaksik, O., Pharmaceuticals' sorptions relative to properties of thirteen different soils. Science of the Total Environment 511 (2015) 435-443.

Designing sustainable soils in Earth's critical zone

NASA Astrophysics Data System (ADS)

Banwart, Steven Allan; de Souza, Danielle Maia; Menon, Manoj; Nikolaidis, Nikolaos; Panagos, Panos; Vala Ragnardsdottir, Kristin; Rousseva, Svelta; van Gaans, Pauline

2014-05-01

The demographic drivers of increasing human population and wealth are creating tremendous environmental pressures from growing intensity of land use, resulting in soil and land degradation worldwide. Environmental services are provided through multiple soil functions that include biomass production, water storage and transmission, nutrient transformations, contaminant attenuation, carbon and nitrogen storage, providing habitat and maintaining the genetic diversity of the land environment. One of the greatest challenges of the 21st century is to identify key risks to soil, and to design mitigation strategies to manage these risks and to enhance soil functions that can last into the future. The scientific study of Earth's Critical Zone (CZ), the thin surface layer that extends vertically from the top of the tree canopy to the bottom of aquifers, provides an essential integrating scientific framework to study, protect and enhance soil functions. The research hypothesis is that soil structure, the geometric architecture of solids, pores and biomass, is a critical indicator and essential factor of productive soil functions. The experimental design selects a network of Critical Zone Observatories (CZOs) as advanced field research sites along a gradient of land use intensity in order to quantify soil structure and soil processes that dictate the flows and transformations of material and energy as soil functions. The CZOs focus multidisciplinary expertise on soil processes, field observation and data interpretation, management science and ecological economics. Computational simulation of biophysical processes provides a quantitative method of integration for the range of theory and observations that are required to quantify the linkages between changes in soil structure and soil functions. Key results demonstrate that changes in soil structure can be quantified through the inputs of organic carbon and nitrogen from plant productivity and microbial activity, coupled with particle aggregation dynamics and organic matter mineralization. Simulation results show that soil structure is highly dynamic and is sensitive to organic matter production and minearlisation rates as influenced by vegetation, tillage and organic carbon amendments. These results point to a step-change in the capability to design soil management and land use through computational simulation. This approach of "sustainability by design" describes the mechanistic process linkages that exist between the above-ground inputs to the CZ and the internal processes that produce soil functions. This approach provides a rational, scientific approach to selecting points of intervention with the CZ in order to design methods to mitigate soil threats and to enhance and sustain vital soil functions. Furthermore, this approach provides a successful pilot study to the use of international networks of CZOs as a planetary-scale laboratory to test the response of CZ process rates along gradients of global environmental change - and to test adaptation strategies to manage the risks arising from the CZ impacts. Acknowledgements. The authors acknowledge the substantial contributions of the entire team of investigators and funding of the SoilTrEC project (EC FP7, agreement no. 244118; www.soiltrec.eu).

Short-term C mineralization (aka the flush of CO2) as an indicator of soil biological health

USDA-ARS?s Scientific Manuscript database

Soil biological activity is a key component of soil health assessments, as it (a) indicates soil nutrient cycling capacity from various organic matter sources to inorganic availability, (b) relates to soil structural conditions, (c) informs about the potential to harbor biodiversity in soil, and (d)...

Mapping of Soil-Ecological Conditions of a Medium-Size Industrial City (Birobidzhan City, Jewish Autonomous Oblast, FarEast of Russia as an Example)

NASA Astrophysics Data System (ADS)

Kalmanova, V. B.; Matiushkina, L. A.

2018-01-01

The authors analyze soil relations with other elements of the city ecosystem (the position in the landscape, soil-forming rocks and lithology, vegetation and its state) to develop the legend and map of soils in the City of Birobidzhan (scale 1:25 000). The focus of study is the morphological structure of urban soils with different degree of disturbance of these relations under the impact of technical effects, economic and recreational activities of the city population. The soil cover structure is composed of four large ecological groups of soils: natural untransformed, natural with a disturbed surface, anthropogenic soils and technogenic surface formations. Using cartometry of the mapped soil contours the authors created the scheme of soil-ecological city zoning, which in a general way depicts the state of soil ecological functions in the city as well as identified zones of soils with preserved, partially and fully distured ecological functions and zones of local geochemical anomalies at the initial formation stage (environmental risk zones).

Cylindrical fabric-confined soil structures

NASA Astrophysics Data System (ADS)

Harrison, Richard A.

A cylindrical fabric-soil structural concept for implementation on the moon and Mars which provides many advantages is proposed. The most efficient use of fabric is to fashion it into cylindrical tubes, creating cylindrical fabric-confined soil structures. The length, diameter, and curvature of the tubes will depend on the intended application. The cylindrical hoop forces provide radial confinement while end caps provide axial confinement. One of the ends is designed to allow passage of the soil into the fabric tube before sealing. Transportation requirements are reduced due to the low mass and volume of the fabric. Construction requirements are reduced due to the self-erection capability via the pneumatic exoskeleton. Maintenance requirements are reduced due to the passive nature of the concept. The structure's natural ductility is well suited for any seismic activity.

PLFA profiling of microbial community structure and seasonal shifts in soils of a Douglas-fir chronosequence

Treesearch

Jennifer Moore-Kucera; Richard P. Dick

2008-01-01

The impact and frequency of forest harvesting could significantly affect soil microbial community (SMC) structure and functioning. The ability of soil microorganisms to perform biogeochemical processes is critical for sustaining forest productivity and has a direct impact on decomposition dynamics and carbon storage potential. The Wind River Canopy Crane Research...

Dynaflow User’s Guide

DTIC Science & Technology

1988-11-01

264 ANALYSIS RESTART. ............. ..... ....... 269 1.0 TITLE CARD. .............. ............. 271 2.0 CONTROL CARDS...stress soil model will provide a tool for such analysis of waterfront structures. To understand the significance of liquefaction, it is important to note...Implementing this effective stress soil model into a finite element computer program would allow analysis of soil and structure together. TECHNICAL BACKGROUND

Microbial community structure and abundance in the rhizosphere and bulk soil of a tomato cropping system that includes cover crops

USDA-ARS?s Scientific Manuscript database

In this report we use Terminal Restriction Fragment Length Polymorphisms (TRFLP) in a tomato production system to “finger printing” the soil microbial community structure with Phylum specific primer sets. Factors influencing the soil microbes are a cover crop of Hairy Vetch (Vicia villosa) or Rye (...

Effects of vegetation structure on soil carbon, nutrients and greenhouse gas exchange in a savannah ecosystem of Mount Kilimanjaro Region

NASA Astrophysics Data System (ADS)

Becker, J.

2015-12-01

The savannah biome is a hotspot for biodiversity and wildlife conservation in Africa and recently got in the focus of research on carbon sequestration. Savannah ecosystems are under strong pressure from climate and land-use change, especially around populous areas like the Mt. Kilimanjaro region. Savannah vegetation consists of grassland with isolated trees and is therefore characterized by high spatial variation of canopy cover, aboveground biomass and root structure. The canopy structure is a major regulator for soil ecological parameters and soil-atmospheric trace gas exchange (CO2, N2O, CH4) in water limited environments. The spatial distribution of these parameters and the connection between above and belowground processes are important to understand and predict ecosystem changes and estimate its vulnerability. Our objective was to determine spatial trends and changes of soil parameters and relate their variability to the vegetation structure. We chose three trees from each of the two most dominant species (Acacia nilotica and Balanites aegyptiaca) in our research area. For each tree, we selected transects with nine sampling points of the same relative distances to the stem. At these each sampling point a soil core was taken and separated in 0-10 cm and 10-30 cm depth. We measured soil carbon (C) and nitrogen (N) storage, microbial biomass C and N, Natural δ13C, soil respiration, available nutrients, pH, cation exchange capacity (CEC) as well as root biomass and -density, soil temperature and soil water content. Concentrations and stocks of C and N fractions, CEC and K+ decreased up to 50% outside the crown covered area. Microbial C:N ratio and CO2 efflux was about 30% higher outside the crown. This indicates N limitation and low C use efficiency in soil outside the crown area. We conclude that the spatial structure of aboveground biomass in savanna ecosystems leads to a spatial variance in nutrient limitation. Therefore, the capability of a savanna ecosystem to act as a C sink is directly and indirectly dependent on the vegetation structure.

Energy Transformations of Soil Organic Matter in a Changing World

NASA Astrophysics Data System (ADS)

Herrmann, A. M.; Coucheney, E.; Grice, S. M.; Ritz, K.; Harris, J.

2011-12-01

The role of soils in governing the terrestrial carbon balance is acknowledged as being important but remains poorly understood within the context of climate change. Soils exchange energy with their surroundings and are therefore open systems thermodynamically, but little is known how energy transformations of decomposition processes are affected by temperature. Soil organic matter and the soil biomass can be conceptualised as analogous to the 'fuel' and 'biological engine' of the earth, respectively, and are pivotal in driving the belowground carbon cycle. Thermodynamic principles of soil organic matter decomposition were evaluated by means of isothermal microcalorimetry (TAM Air, TA Instruments, Sollentuna Sweden: (i) Mineral forest soils from the Flakaliden long-term nitrogen fertilisation experiment (Sweden) were amended with a range of different substrates representing structurally simple to complex, ecologically pertinent organic matter and heat signatures were determined at temperatures between 5 and 25°C. (ii) Thermodynamic and resource-use efficiencies of the biomass were determined in arable soils which received contrasting long-term management regimes with respect to organic matter and nitrogen since 1956. The work showed that (i) structurally labile components have higher activation energy and temperature dependence than structurally more complex organic components. This is, however, in contrast to the thermodynamic argument which suggests the opposite that reactions metabolising structurally complex, aromatic components have higher temperature dependence than reactions metabolising structurally more labile components. (ii) Microbial communities exposed to long-term stress by heavy metal and low pH were less thermodynamic efficient and showed a decrease in resource-use efficiency in comparison with conventional input regimes. Differences in efficiencies were mirrored in both the phenotypic and functional profiles of the communities. We will present our findings illustrating the capacity of isothermal microcalorimetry to evaluate temperature dependencies of soil organic matter decomposition, associated energy transformations and thermodynamic principles in soil ecosystems.

Dissecting the multi-scale spatial relationship of earthworm assemblages with soil environmental variability.

PubMed

Jiménez, Juan J; Decaëns, Thibaud; Lavelle, Patrick; Rossi, Jean-Pierre

2014-12-05

Studying the drivers and determinants of species, population and community spatial patterns is central to ecology. The observed structure of community assemblages is the result of deterministic abiotic (environmental constraints) and biotic factors (positive and negative species interactions), as well as stochastic colonization events (historical contingency). We analyzed the role of multi-scale spatial component of soil environmental variability in structuring earthworm assemblages in a gallery forest from the Colombian "Llanos". We aimed to disentangle the spatial scales at which species assemblages are structured and determine whether these scales matched those expressed by soil environmental variables. We also tested the hypothesis of the "single tree effect" by exploring the spatial relationships between root-related variables and soil nutrient and physical variables in structuring earthworm assemblages. Multivariate ordination techniques and spatially explicit tools were used, namely cross-correlograms, Principal Coordinates of Neighbor Matrices (PCNM) and variation partitioning analyses. The relationship between the spatial organization of earthworm assemblages and soil environmental parameters revealed explicitly multi-scale responses. The soil environmental variables that explained nested population structures across the multi-spatial scale gradient differed for earthworms and assemblages at the very-fine- (<10 m) to medium-scale (10-20 m). The root traits were correlated with areas of high soil nutrient contents at a depth of 0-5 cm. Information on the scales of PCNM variables was obtained using variogram modeling. Based on the size of the plot, the PCNM variables were arbitrarily allocated to medium (>30 m), fine (10-20 m) and very fine scales (<10 m). Variation partitioning analysis revealed that the soil environmental variability explained from less than 1% to as much as 48% of the observed earthworm spatial variation. A large proportion of the spatial variation did not depend on the soil environmental variability for certain species. This finding could indicate the influence of contagious biotic interactions, stochastic factors, or unmeasured relevant soil environmental variables.

Prototype reinforced soil embankment for reconstruction of US route 62 slope failure in Chickasha, OK.

DOT National Transportation Integrated Search

2015-01-01

One of the main concerns in internal stability of reinforced soil structures constructed with fine-grained or : marginal quality soils is the change in shear strength of the soil-reinforcement interface when the soil gravimetric water : content (GWC)...

Prototype reinforced soil embankment for reconstruction of US 62 slope failure in Chickasha, OK.

DOT National Transportation Integrated Search

2013-05-01

One of the main concerns in internal stability of reinforced soil structures constructed with fine-grained or marginal quality soils is the change in shear strength of the soil-reinforcement interface when the soil gravimetric water content (GWC) inc...

Effects of biochar blends on microbial community composition in two coastal plain soils

EPA Science Inventory

The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

PubMed Central

Leite, Márcio F. A.; Pan, Yao; Bloem, Jaap; Berge, Hein ten; Kuramae, Eiko E.

2017-01-01

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake. PMID:28198425

Soil microbial succession along a chronosequence on a High Arctic glacier foreland, Ny-Ålesund, Svalbard: 10 years' change

NASA Astrophysics Data System (ADS)

Yoshitake, Shinpei; Uchida, Masaki; Iimura, Yasuo; Ohtsuka, Toshiyuki; Nakatsubo, Takayuki

2018-06-01

Rapid glacial retreat in the High Arctic causes the expansion of new habitats, but the successional trajectories of soil microbial communities are not fully understood. We examined microbial succession along a chronosequence twice with a 10-year interval in a High Arctic glacier foreland. Soil samples were collected from five study sites with different ages and phospholipid fatty acids analysis was conducted to investigate the microbial biomass and community structure. Microbial biomass did not differ significantly between the two sampling times but tended to increase with the chronosequence and showed a significant correlation with soil carbon (C) and nitrogen (N) content. Microbial community structure clearly differed along the chronosequence and was correlated with C and N content. The largest shift in community structure over 10 years was observed in the newly exposed sites after deglaciation. The accumulation of soil organic matter was regarded as an important determinant both of microbial biomass and community structure over the successional period. In contrast, the initial microbial community on the newly exposed soil changed rapidly even in the High Arctic, suggesting that some key soil processes such as C and N cycling can also shift within the relatively short period after rapid glacial retreat.

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

PubMed

Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Plant diversity and root traits benefit physical properties key to soil function in grasslands.

PubMed

Gould, Iain J; Quinton, John N; Weigelt, Alexandra; De Deyn, Gerlinde B; Bardgett, Richard D

2016-09-01

Plant diversity loss impairs ecosystem functioning, including important effects on soil. Most studies that have explored plant diversity effects belowground, however, have largely focused on biological processes. As such, our understanding of how plant diversity impacts the soil physical environment remains limited, despite the fundamental role soil physical structure plays in ensuring soil function and ecosystem service provision. Here, in both a glasshouse and a long-term field study, we show that high plant diversity in grassland systems increases soil aggregate stability, a vital structural property of soil, and that root traits play a major role in determining diversity effects. We also reveal that the presence of particular plant species within mixed communities affects an even wider range of soil physical processes, including hydrology and soil strength regimes. Our results indicate that alongside well-documented effects on ecosystem functioning, plant diversity and root traits also benefit essential soil physical properties. © 2016 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.

[Priming effect of biochar on the minerialization of native soil organic carbon and the mechanisms: A review.

PubMed

Chen, Ying; Liu, Yu Xue; Chen, Chong Jun; Lyu, Hao Hao; Wa, Yu Ying; He, Li Li; Yang, Sheng Mao

2018-01-01

In recent years, studies on carbon sequestration of biochar in soil has been in spotlight owing to the specific characteristics of biochar such as strong carbon stability and well developed pore structure. However, whether biochar will ultimately increase soil carbon storage or promote soil carbon emissions when applied into the soil? This question remains controversial in current academic circles. Further research is required on priming effect of biochar on mineralization of native soil organic carbon and its mechanisms. Based on the analysis of biochar characteristics, such as its carbon composition and stability, pore structure and surface morphology, research progress on the priming effect of biochar on the decomposition of native soil organic carbon was reviewed in this paper. Furthermore, possible mechanisms of both positive and negative priming effect, that is promoting and suppressing the mineralization, were put forward. Positive priming effect is mainly due to the promotion of soil microbial activity caused by biochar, the preferential mineralization of easily decomposed components in biochar, and the co-metabolism of soil microbes. While negative priming effect is mainly based on the encapsulation and adsorption protection of soil organic matter due to the internal pore structure and the external surface of biochar. Other potential reasons for negative priming effect can be the stabilization resulted from the formation of organic-inorganic complex promoted by biochar in the soil, and the inhibition of activity of soil microbes and its enzymes by biochar. Finally, future research directions were proposed in order to provide theoretical basis for the application of biochar in soil carbon sequestration.

Principles of control automation of soil compacting machine operating mechanism

NASA Astrophysics Data System (ADS)

Anatoly Fedorovich, Tikhonov; Drozdov, Anatoly

2018-03-01

The relevance of the qualitative compaction of soil bases in the erection of embankment and foundations in building and structure construction is given.The quality of the compactible gravel and sandy soils provides the bearing capability and, accordingly, the strength and durability of constructed buildings.It has been established that the compaction quality depends on many external actions, such as surface roughness and soil moisture; granulometry, chemical composition and degree of elasticity of originalfilled soil for compaction.The analysis of technological processes of soil bases compaction of foreign and domestic information sources showed that the solution of such important problem as a continuous monitoring of soil compaction actual degree in the process of machine operation carry out only with the use of modern means of automation. An effective vibrodynamic method of gravel and sand material sealing for the building structure foundations for various applications was justified and suggested.The method of continuous monitoring the soil compaction by measurement of the amplitudes and frequencies of harmonic oscillations on the compactible surface was determined, which allowed to determine the basic elements of facilities of soil compacting machine monitoring system of operating, etc. mechanisms: an accelerometer, a bandpass filter, a vibro-harmonics, an on-board microcontroller. Adjustable parameters have been established to improve the soil compaction degree and the soil compacting machine performance, and the adjustable parameter dependences on the overall indexhave been experimentally determined, which is the soil compaction degree.A structural scheme of automatic control of the soil compacting machine control mechanism and theoperation algorithm has been developed.

Native soil organic matter conditions the response of microbial communities to organic inputs with different stability

NASA Astrophysics Data System (ADS)

Yanardaǧ, Ibrahim H.; Zornoza, Raúl; Bastida, Felipe; Büyükkiliç-Yanardaǧ, Asuman; Acosta, Jose A.; García, Carlos; Faz, Ángel; Mermut, Ahmet R.

2017-04-01

The response of soil microbial communities from soils with different soil organic matter (SOM) content to organic inputs with different stability is still poorly understood. Thus, an incubation experiment was designed to study how the addition of pig slurry (PS), its manure (M) and its biochar (BC) affect soil microbial community and activity in three soils differing in SOM content (Regosol, Luvisol and Kastanozem). The evolution of different C and N fractions, microbial biomass C and N, enzyme activities and microbial community structure by the use of phospholipid fatty acid (PLFA) analysis was assessed for 60 days. Results showed that the different amendments had different effect on microbial properties depending on the soil type. The addition of M caused the highest increase in all microbial properties in the three soils, followed by PS. These changes were more intense in the soil with the lowest SOM (Regosol). The addition of M and PS caused changes in the microbial community structure in all soils, which were more related to the presence of available sources of N than to the labile fractions of C. The addition of BC was followed by increases in the proportions of fungi and Gram positive bacteria in the Regosol, while enhanced the proportion of actinobacteria in all soil types, related to increments in pH and soil C recalcitrance. Thus, native SOM determined the response of microbial communities to external inputs with different stability, soils with low SOM being more prone to increase microbial biomass and activity and change microbial community structure.

Effects of soil water repellency on microbial community structure and functions in Mediterranean pine forests

NASA Astrophysics Data System (ADS)

Lozano, Elena; Grayston, Sue J.; Mataix-Solera, Jorge; Arcenegui, Victoria; Jimenez-Pinilla, Patricia; Mataix-Beneyto, Jorge

2015-04-01

Soil water repellency (SWR) is a property commonly observed in forest areas showing wettable and water repellent patches with high spatial variability. SWR can greatly influence the hydrology and the ecology of forest soils. The capacity of soil microorganisms to degrade different organic compounds depends upon species composition, so this may affect changes in SWR on the microsite scale (such as the presence of soil water repellent patches; Mülleret al., 2010). In the Mediterranean forest context, SWR has been found to be related to microbial community composition. The accumulation of different hydrophobic compounds might be causing the shifts in microbial community structure (Lozano et al., 2014). In this study we investigated the effects of SWR persistence on soil microbial community structure and enzyme activity under Pinus halepensis forest in three different sites: Petrer, Gorga and Jávea (Alicante, E Spain). Soil samples were classified into three different water repellency classes (wettable, slight or strongly water repellent samples) depending on the SWR persistence. The soil microbial community was determined through phospholipid fatty acids (PLFAs). Enzyme activities chosen for this study were cellulase, β-glucosidase and N-acetyl-β-glucosaminide (NAG). The relationships between microbiological community structure and some soil properties such as pH, Glomalin Related Soil Protein, soil organic matter content and soil respiration were also studied. Redundancy analyses and decomposition of the variances were performed to clarify how microbial community composition and enzyme activities are affected by SWR and soil properties. The effect of SWR on microbial community composition differed between locations. This effect was clearer in the Petrer site. Enzyme activity varied considerably depending on SWR persistence. The highest activities were found in slightly SWR samples and the lowest mostly in the strongly water repellent ones. These preliminary results suggest a possible influence of SWR on microbial structure and its activity in soils. References: Lozano, E., García-Orenes, F., Bárcenas-Moreno, G., Jiménez-Pinilla, P., Mataix-Solera, J., Arcenegui, V., Morugán-Coronado, A., Mataix-Beneyto, J., 2014. Relationships between soil water repellency and microbial community composition under different plant species in a Mediterranean semiarid forest. J. Hydrol. Hydromech., 62, 101-107 Müller, K., Deurer, M., Newton, P.C.D., 2010. Is there a link between elevated atmospheric carbon dioxide concentration, soil water repellency and soil carbon mineralization? Agric. Ecosyst. Environ., 139, 98-109. Acknowledgements: to the "Ministerio de Economía and Competitividad" of Spanish Government for finance the POSTFIRE project (CGL2013- 47862-C2-1-R), Generalitat Valenciana for PhD grant, and Spanish Soil Science Society and FUEGORED for their support.

Minute tubular forms in soil

NASA Technical Reports Server (NTRS)

Casida, L. E., Jr.; Liu, K.-C.

1979-01-01

Large numbers of long, straight, flattened structures were observed during an electron-microscope study of bacteriophage in aqueous extracts. These structures were called tubules and ranged in width from 10 to 50 nm. Materials and methods were discussed relative to extraction of tubules from soil, electron microscopy, quantitation of tubules in filtrate suspension, tests performed on tubules, plaque formation, and nutrient amendments. It is found that all of the tubules recovered from soil are broken at one or both ends. They are present in surface soils but not in a subsurface sample. Their numbers decrease during bacterial multiplication in soil or broth-containing soil. The tubules appear to be composed of protein that could be disintegrated to liberate nonprotein fibers. A possible clue to the nature of the tubules is their apparent relation to soil bacteria.

Changes in the Metagenome of Prokaryotic Community as an Indicator of Fertility of Arable Soddy-Podzolic Soils upon Fertilizer Application

NASA Astrophysics Data System (ADS)

Naliukhin, A. N.; Khamitova, S. M.; Glinushkin, A. P.; Avdeev, Yu. M.; Snetilova, V. S.; Laktionov, Yu. V.; Surov, V. V.; Siluyanova, O. V.; Belozerov, D. A.

2018-03-01

The influence of different systems of fertilization and liming on the changes in the taxonomic structure of prokaryotic community in arable soddy-podzolic soil (Albic Retisol (Loamic, Aric, Cutanic, Differentic, Ochric)) was studied in a stationary field experiment of Vologda State Dairy Farming Academy with the use of high-performance sequencing method of gene 16S rRNA. The 25-year-old fallow plot, in which the intensity of microbiological processes was close to that in the virgin soddy-podzolic soils, was used as a control. At the first stage, dominant phyla were identified: Proteobacteria (45.3-56.2%), Actinobacteria (13.6-20.4%), Bacteroidetes (7.2-19.3%), Acidobacteria (7.1-11.5%), and Verrucomicrobia (4.3-10.3%). Several groups of microorganisms-indicators, whose portion changes in the arable soil under the influence of liming, fertilizer application, and soil treatment in comparison with the control, were determined. The applied approach made it possible to relate the taxonomic structure of the soil microbial cenosis with external factors for assessing changes in the structure of soil microbial complex under the impact of different uses of the arable soil.

A soil-landscape framework for understanding spatial and temporal variability in biogeochemical processes in catchments

NASA Astrophysics Data System (ADS)

McGuire, K. J.; Bailey, S. W.; Ross, D. S.

2017-12-01

Heterogeneity in biophysical properties within catchments challenges how we quantify and characterize biogeochemical processes and interpret catchment outputs. Interactions between the spatiotemporal variability of hydrological states and fluxes and soil development can spatially structure catchments, leading to a framework for understanding patterns in biogeochemical processes. In an upland, glaciated landscape at the Hubbard Brook Experimental Forest (HBEF) in New Hampshire, USA, we are embracing the structure and organization of soils to understand the spatial relations between runoff production zones, distinct soil-biogeochemical environments, and solute retention and release. This presentation will use observations from the HBEF to demonstrate that a soil-landscape framework is essential in understanding the spatial and temporal variability of biogeochemical processes in this catchment. Specific examples will include how laterally developed soils reveal the location of active runoff production zones and lead to gradients in primary mineral dissolution and the distribution of weathering products along hillslopes. Soil development patterns also highlight potential carbon and nitrogen cycling hotspots, differentiate acidic conditions, and affect the regulation of surface water quality. Overall, this work demonstrates the importance of understanding the landscape-level structural organization of soils in characterizing the variation and extent of biogeochemical processes that occur in catchments.

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

PubMed Central

Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong

2017-01-01

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654

[Community structure of soil fauna in Eucalyptus grandis plantations at different slope locations].

PubMed

Zhao, Yu; Zhong, Yu; Zhang, Jian; Yang, Wan-qin

2010-09-01

To understand the effects of slope location on the community structure of soil fauna in Eucalyptus grandis plantation, an investigation was made on the soil fauna in 3 E. grandis plantations at different slope locations in the hilly area of Sichuan Province from January to October 2009. A total of 39,2762 individuals were observed, belonging to 146 groups, 7 phyla, 16 classes, and 31 orders. The community composition, trophic group, diversity, and seasonal dynamics of soil fauna in the plantations all varied with slope. The abundance of macro-fauna, xeric meso- and micro-fauna, saprophagous macro-fauna, and omnivorous xeric meso- and micro-fauna increased with the decrease of slope, indicating that soil fauna had sensitive responses to the soil environmental factors affected by slope. Significant differences in the diversity of soil saprophagous macro-fauna and hygrophilous meso- and micro-fauna were observed at different slope locations, suggesting that these two faunal groups could be used as the indicators of the habitat heterogeneity of E. grandis plantations at different slope. Overall, slope location had definite effects on the community structure and distribution of soil fauna in the E. grandis plantations, but the effects were not statistically significant.

Coal mining activities change plant community structure due to air pollution and soil degradation.

PubMed

Pandey, Bhanu; Agrawal, Madhoolika; Singh, Siddharth

2014-10-01

The aim of this study was to investigate the effects of coal mining activities on the community structures of woody and herbaceous plants. The response of individual plants of community to defilement caused by coal mining was also assessed. Air monitoring, soil physico-chemical and phytosociological analyses were carried around Jharia coalfield (JCF) and Raniganj coalfield. The importance value index of sensitive species minified and those of tolerant species enhanced with increasing pollution load and altered soil quality around coal mining areas. Although the species richness of woody and herbaceous plants decreased with higher pollution load, a large number of species acclimatized to the stress caused by the coal mining activities. Woody plant community at JCF was more affected by coal mining than herbaceous community. Canonical correspondence analysis revealed that structure of herbaceous community was mainly driven by soil total organic carbon, soil nitrogen, whereas woody layer community was influenced by sulphur dioxide in ambient air, soil sulphate and soil phosphorus. The changes in species diversity observed at mining areas indicated an increase in the proportion of resistant herbs and grasses showing a tendency towards a definite selection strategy of ecosystem in response to air pollution and altered soil characteristics.

Resource seeking strategies of zoosporic true fungi in heterogeneous soil habitats at the microscale level

PubMed Central

Gleason, Frank H.; Crawford, John W.; Neuhauser, Sigrid; Henderson, Linda E.; Lilje, Osu

2012-01-01

Zoosporic true fungi have frequently been identified in samples from soil and freshwater ecosystems using baiting and molecular techniques. In fact some species can be components of the dominant groups of microorganisms in particular soil habitats. Yet these microorganisms have not yet been directly observed growing in soil ecosystems. Significant physical characteristics and features of the three-dimensional structures of soils which impact microorganisms at the microscale level are discussed. A thorough knowledge of soil structures is important for studying the distribution of assemblages of these fungi and understanding their ecological roles along spatial and temporal gradients. A number of specific adaptations and resource seeking strategies possibly give these fungi advantages over other groups of microorganisms in soil ecosystems. These include chemotactic zoospores, mechanisms for adhesion to substrates, rhizoids which can penetrate substrates in small spaces, structures which are resistant to environmental extremes, rapid growth rates and simple nutritional requirements. These adaptations are discussed in the context of the characteristics of soils ecosystems. Recent advances in instrumentation have led to the development of new and more precise methods for studying microorganisms in three-dimensional space. New molecular techniques have made identification of microbes possible in environmental samples. PMID:22308003

Water regime history drives responses of soil Namib Desert microbial communities to wetting events

NASA Astrophysics Data System (ADS)

Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

2015-07-01

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

Water regime history drives responses of soil Namib Desert microbial communities to wetting events.

PubMed

Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A

2015-07-21

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

The importance of humin in soil characterisation: A study on Amazonian soils using different fluorescence techniques.

PubMed

Tadini, Amanda Maria; Nicolodelli, Gustavo; Mounier, Stephane; Montes, Célia Regina; Milori, Débora Marcondes Bastos Pereira

2015-12-15

Soil organic matter (SOM) is a complex mixture of molecules with different physicochemical properties, with humic substances (HS) being the main component as it represents around 20-50% of SOM structure. Soil of the Amazon region is considered one of the larger carbon pools of the world; thus, studies of the humic fractions are important for understanding the dynamics of organic matter (OM) in these soils. The aim of this study was to use laser-induced fluorescence spectroscopy (LIFS) and a combination of excitation-emission matrix (EEM) fluorescence with Parallel Factor Analysis (CP/PARAFAC) to assess the characteristics of humin (HU) extracted from Amazonian soils. The results obtained using LIFS showed that there was an increasing gradient of humification degree with depth, the deeper horizon presenting a higher amount of aromatic groups in the structure of HU. From the EEM, the contribution of two fluorophores with similar behaviour in the structures of HU and whole soil was assessed. Additionally, the results showed that the HU fraction might represent a larger fraction of SOM than previously thought: about 80-93% of some Amazon soils. Therefore, HU is an important humic fraction, thus indicating its role in environmental analysis, mainly in soil analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Visualizing Rhizosphere Soil Structure Around Living Roots

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2008-12-01

The rhizosphere, a thin layer of soil (0 to 2 mm) surrounding a living root, is an important interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 ìm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

Seismic behavior of breakwaters on complex ground by numerical tests: Liquefaction and post liquefaction ground settlements

NASA Astrophysics Data System (ADS)

Gu, Linlin; Zhang, Feng; Bao, Xiaohua; Shi, Zhenming; Ye, Guanlin; Ling, Xianzhang

2018-04-01

A large number of breakwaters have been constructed along coasts to protect humans and infrastructures from tsunamis. There is a risk that foundation soils of these structures may liquefy, or partially liquefy during the earthquake preceding a tsunami, which would greatly reduce the structures' capacity to resist the tsunami. It is necessary to consider not only the soil's liquefaction behavior due to earthquake motions but also its post-liquefaction behavior because this behavior will affect the breakwater's capacity to resist an incoming tsunami. In this study, numerical tests based on a sophisticated constitutive model and a soil-water coupled finite element method are used to predict the mechanical behavior of breakwaters and the surrounding soils. Two real breakwaters subjected to two different seismic excitations are examined through numerical simulation. The simulation results show that, earthquakes affect not only the immediate behavior of breakwaters and the surrounding soils but also their long-term settlements due to post-earthquake consolidation. A soil profile with thick clayey layers beneath liquefied soil is more vulnerable to tsunami than a soil profile with only sandy layers. Therefore, quantitatively evaluating the seismic behavior of breakwaters and surrounding soils is important for the design of breakwater structures to resist tsunamis.

Rhizospheric effects on the microbial community of e-waste-contaminated soils using phospholipid fatty acid and isoprenoid glycerol dialkyl glycerol tetraether analyses.

PubMed

Song, Mengke; Cheng, Zhineng; Luo, Chunling; Jiang, Longfei; Zhang, Dayi; Yin, Hua; Zhang, Gan

2018-04-01

We performed the study of rhizospheric effects on soil microbial community structure, including bacteria, fungi, actinomycete, and archaea, at an electronic waste (e-waste) recycling site by analyzing the phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether (GDGT) contents. By comparing PLFA and isoprenoid GDGT profiles of rhizospheric and surrounding bulk soils of 11 crop species, we observed distinct microbial community structures. The total PLFA concentration was significantly higher in rhizospheric soils than in non-rhizospheric soils, whereas no obvious difference was found in the total isoprenoid GDGT concentrations. The microbial community structure was also different, with higher ratios of fungal-to-bacterial PLFAs (F/B) and lower relative abundance of Gram-positive bacteria in rhizospheric soils. The extent of rhizospheric effects varied among plant species, and Colocasia esculenta L. had the greatest positive effects on the total microbial biomass. Dissolved organic carbon and pH were the main environmental factors affecting the microbial community represented by PLFAs, while the archaeal community was influenced by copper and zinc in all soils. These results offer a comprehensive view of rhizospheric effects on microbes in heavy metal and persistent organic pollutant co-contaminated soil, and provide fundamental knowledge regarding microbial ecology in e-waste-contaminated soils.

Evidence for the functional significance of diazotroph community structure in soil.

PubMed

Hsu, Shi-Fang; Buckley, Daniel H

2009-01-01

Microbial ecologists continue to seek a greater understanding of the factors that govern the ecological significance of microbial community structure. Changes in community structure have been shown to have functional significance for processes that are mediated by a narrow spectrum of organisms, such as nitrification and denitrification, but in some cases, functional redundancy in the community seems to buffer microbial ecosystem processes. The functional significance of microbial community structure is frequently obscured by environmental variation and is hard to detect in short-term experiments. We examine the functional significance of free-living diazotrophs in a replicated long-term tillage experiment in which extraneous variation is minimized and N-fixation rates can be related to soil characteristics and diazotroph community structure. Soil characteristics were found to be primarily impacted by tillage management, whereas N-fixation rates and diazotroph community structure were impacted by both biomass management practices and interactions between tillage and biomass management. The data suggest that the variation in diazotroph community structure has a greater impact on N-fixation rates than do soil characteristics at the site. N-fixation rates displayed a saturating response to increases in diazotroph community diversity. These results show that the changes in the community structure of free-living diazotrophs in soils can have ecological significance and suggest that this response is related to a change in community diversity.

[Community structure of soil meso- and micro-fauna in different habitats of urbanized region].

PubMed

Qin, Zhong; Zhang, Jia-en; Li, Qing-fang

2009-12-01

Investigations were made in May, June, and November 2007 and January 2008 to study the structural characteristics and their seasonal variations of soil meso- and micro-fauna communities in six habitats of three land use types (forest land, constructed grassland and farmland) in Tianhe District of Guangzhou City. The horizontal spatial distribution of soil fauna differed with habitat. During the investigation periods, the Botanical Garden of South China Agricultural University had the highest individual number (1286) of soil mesa- and micro-fauna, while the farmland, especially in the Fenghuang Street area, had the lowest number of individuals and groups. The seasonal variation of the individual number was in order of autumn (1815) > spring (1623) > winter (1365) > summer (1276). Hierarchical clustering and detrended correspondence analysis also showed that the community composition of soil meso- and micro-fauna in different habitats exhibited distinct seasonal variation. In the same seasons, the community structure and composition of soil meso- and micro-fauna in different habitats were correlated to the degrees of human interferences and the properties of soil environment.

Soil ecology of a rock outcrop ecosystem: Abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades

USGS Publications Warehouse

Cartwright, Jennifer M.; Advised by Dzantor, E. Kudjo

2015-01-01

Stress factors quantified by this research include shallow soil (depth to bedrock ranging from 2.4 to 22.6 cm), volumetric soil water content levels seasonally ranging from xeric (below 5%) to saturated (above 50%), and seasonally extreme ground-surface temperatures (above 48°C). Findings from this research indicate that spatial and temporal heterogeneity exists in limestone cedar glades in terms of abiotic stress factors and soil physical and chemical properties. Several such soil properties (e.g. soil depth, organic matter levels, pH, and particle size distribution) are spatially correlated. These soil properties were statistically related to ecological structures and functions such as vegetation patterns, soil respiration, the density of culturable heterotrophic microbes in soil and metabolic diversity of soil microbial community profiles. In general, zones within limestone cedar glades that had relatively shallow soil, alkaline pH, low levels of organic matter and high levels of silt also tended to have depressed rates of soil respiration and reduced densities and metabolic diversity of culturable heterotrophic soil microbes. Additionally, seasonally-relevant stress factors including soil water content and temperatures at or near the soil surface were related to the same set of ecological structures and functions.

Simulating root-induced rhizosphere deformation and its effect on water flow

NASA Astrophysics Data System (ADS)

Aravena, J. E.; Ruiz, S.; Mandava, A.; Regentova, E. E.; Ghezzehei, T.; Berli, M.; Tyler, S. W.

2011-12-01

Soil structure in the rhizosphere is influenced by root activities, such as mucilage production, microbial activity and root growth. Root growth alters soil structure by moving and deforming soil aggregates, affecting water and nutrient flow from the bulk soil to the root surface. In this study, we utilized synchrotron X-ray micro-tomography (XMT) and finite element analysis to quantify the effect of root-induced compaction on water flow through the rhizosphere to the root surface. In a first step, finite element meshes of structured soil around the root were created by processing rhizosphere XMT images. Then, soil deformation by root expansion was simulated using COMSOL Multiphysics° (Version 4.2) considering the soil an elasto-plastic porous material. Finally, fluid flow simulations were carried out on the deformed mesh to quantify the effect of root-induced compaction on water flow to the root surface. We found a 31% increase in water flow from the bulk soil to the root due to a 56% increase in root diameter. Simulations also show that the increase of root-soil contact area was the dominating factor with respect to the calculated increase in water flow. Increase of inter-aggregate contacts in size and number were observed within a couple of root diameters away from the root surface. But their influence on water flow was, in this case, rather limited compared to the immediate soil-root contact.

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa.

PubMed

van Wyk, Deidré A B; Adeleke, Rasheed; Rhode, Owen H J; Bezuidenhout, Carlos C; Mienie, Charlotte

2017-09-01

Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil. Acid phosphatase and β-glucosidase activities were significantly reduced in soils under Bt maize cultivation. The species diversity differed between fields and Bt and non-Bt maize soils. Results revealed that Actinobacteria, Proteobacteria, and Acidobacteria were the dominant phyla present in these soils. Redundancy analyses indicated that some chemical properties and enzyme activities could explain differences in bacterial community structures. Variances existed in microbial community structures between Bt and non-Bt maize fields. There were also differences between the chemical and biochemical properties of rhizosphere soils under Bt and non-Bt maize cultivation. These differences could be related to agricultural practices and cultivar type. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relationship between gaseous N dynamics and the hydraulic state of hierarchically structured soils

NASA Astrophysics Data System (ADS)

Schlüter, Steffen; Dörsch, Peter; Vogel, Hans-Jörg

2017-04-01

The inherent spatial heterogeneity of soil generates spatially distributed micro-sites with different local N gas (NO, N2O, N2) production and release rates. Moreover, local micro-site conditions and the pathways between them depend on soil moisture which itself is highly dynamic close to the soil surface. These relationships need to be taken into account for a quantitative understanding of soil denitrification and associated N gas dynamics. Soil structure has been recognized as a key factor to understand the high spatial variability of N gas emissions. In particular gaseous N release from soils depends on: i) the total denitrification rate, which is related to the spatial extent and distribution of anaerobic sites and ii) the probability of N2O to escape from the soil without being further reduced to N2. This impact of soil structure is typically ignored in studies with soil slurries or repacked soil. In this project we run well-defined mesocosm experiments on N gas dynamics with hierarchically structured, artificial soils in which the spatial distribution of substrate and denitrifiers is known exactly. Sintered, porous glass pellets are inoculated with strains of Paracoccus denitrificans and/or Agrobacterium tumefaciens and amended with nutrient solution. These pellets are embedded in coarse-grained sand within gas-tight columns under O2/He atmosphere. The pellets are either places in layers or randomly to create different patterns of N gas production sites and diffusion pathways. Denitrification occurs in the anaerobic centers of the porous pellets, while the partially saturated sand matrix controls the diffusive transport of N gases towards the headspace, where all relevant gas concentrations are monitored with gas chromatography. Water saturations are adjusted such that the diffusive pathways are either fully continuous or partially discontinuous. Preliminary results indicate that the water content exert a major control on the magnitude of denitrification, whereas the onset and dynamics are mainly controlled by the position of the substrate and the denitrifiers.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate formation could alter how we currently treat our predictions of soil biogeochemistry. Current predictions are largely site- or biome-specific; quantitative mechanisms could underpin "rules" that operate at the pore-scale leading to more robust, mechanistic models.

Farm-scale variation of soil quality indices and association with edaphic properties

USDA-ARS?s Scientific Manuscript database

Soil organisms are indicators of dynamic soil quality because their community structure and population density are sensitive to management changes. However, edaphic properties can also affect soil organisms and high spatial variability can confound their utility for soil evaluation. In the present...

Fall cover crops boost soil arbuscular mycorrhizal fungi which can lead to reduced inputs

USDA-ARS?s Scientific Manuscript database

Fall cover crops provide multiple benefits to producers. These benefits include pathogen and pest protection, drought protection, weed control, reduced soil erosion, nutrient acquisition and retention, increased soil organic matter, and conservation of soil water by improvement of soil structure th...

Development and assessment of transparent soil and particle image velocimetry in dynamic soil-structure interaction

DOT National Transportation Integrated Search

2007-02-01

This research combines Particle Image Velocimetry (PIV) and transparent soil to investigate the dynamic rigid block and soil interaction. In order to get a low viscosity pore fluid for the transparent soil, 12 different types of chemical solvents wer...

Differential effects of fine root morphology on water dynamics in the root-soil interface

NASA Astrophysics Data System (ADS)

DeCarlo, K. F.; Bilheux, H.; Warren, J.

2017-12-01

Soil water uptake form plants, particularly in the rhizosphere, is a poorly understood question in the plant and soil sciences. Our study analyzed the role of belowground plant morphology on soil structural and water dynamics of 5 different plant species (juniper, grape, maize, poplar, maple), grown in sandy soils. Of these, the poplar system was extended to capture drying dynamics. Neutron radiography was used to characterize in-situ dynamics of the soil-water-plant system. A joint map of root morphology and soil moisture was created for the plant systems using digital image processing, where soil pixels were connected to associated root structures via minimum distance transforms. Results show interspecies emergent behavior - a sigmoidal relationship was observed between root diameter and bulk/rhizosphere soil water content difference. Extending this as a proxy for extent of rhizosphere development with root age, we observed a logistic growth pattern for the rhizosphere: minimal development in the early stages is superceded by rapid onset of rhizosphere formation, which then stabilizes/decays with the likely root suberization. Dynamics analysis of water content differences between the root/rhizosphere, and rhizosphere/bulk soil interface highlight the persistently higher water content in the root at all water content and root size ranges. At the rhizosphere/bulk soil interface, we observe a shift in soil water dynamics by root size: in super fine roots, we observe that water content is primarily lower in the rhizosphere under wetter conditions, which then gradually increases to a relatively higher water content under drier conditions. This shifts to a persistently higher rhizosphere water content relative to bulk soil in both wet/dry conditions with increased root size, suggesting that, by size, the finest root structures may contribute the most to total soil water uptake in plants.

Role of model structure on the response of soil biogeochemistry to hydro-climatic fluctuations

NASA Astrophysics Data System (ADS)

Manzoni, S.; Porporato, A.

2005-05-01

Soil carbon and nutrient cycles are strongly affected by hydro-climatic variability, which interacts with the internal ecosystem structure. Here we test the implications of biogeochemical model structure on such dynamics by extending an existing model by the authors and coworkers. When forced by hydro-climatic fluctuations, the different model structures induce specific preferential nutrient paths among the soil pools, which in turn affect nutrient distribution and availability to microbes and plants. In particular, if it is assumed that microbes can directly assimilate organic nitrogen, plants tend to be inferior competitors for nutrients even in well-watered conditions, while if a certain amount of organic nitrogen is assumed to be mineralized without being first incorporated into microbial cells, vegetation can be advantaged over a wide range of soil moisture values. We also investigate the intensification of competition for nutrients (e.g., nitrogen) between plant and soil microbial communities under extreme hydrologic conditions, such as droughts and intense storms. Frequent rainfall events may determine ideal soil moisture conditions for plant uptake, enhancing nitrogen leaching while lowering oxygen concentration and inhibiting microbial activity. During droughts, the soil water potential often drops to the point of hampering the plant nutrient uptake while still remaining high enough for microbial decomposition and nitrogen immobilization. The interplay of microbe and vegetation water stress is investigated in depth as it controls the ability of one community (e.g., plants or soil microbes) to establish competitive advantage on the other. The long-term effects of these dynamics of competition and nutrient allocation are explored under steady-state and stochastic soil moisture conditions to analyze the feedbacks between soil organic matter and vegetation dynamics.

Soil microcosm for testing the effects of chemical pollutants on soil fauna communities and trophic structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parmelee, R.W.; Wentsel, R.S.; Phillips, C.T.

1993-08-01

A microcosm technique is presented that uses community and trophic-level analysis of soil nematodes and microarthropods to determine the effects of chemicals on soil systems. Forest soil was treated with either copper, p-nitrophenol, or trinitrotoluene. Nematodes were sorted into bacterivore, fungivore, herbivore, and omnivore-predator trophic groups, and a hatchling category. Microarthropods were sorted to the acarine suborders Prostigmata, Mesostigmata, and Oribatida; the insectan order Collembola; and a miscellaneous group. Omnivore-predator nematodes and meso-stigmatid and oribatid mites were the groups most sensitive to copper and were significantly reduced at levels as low as 100 [mu]g g[sup [minus]1] copper. Total nematode andmore » microarthropod numbers declined above 200 [mu]g g[sup [minus]1] copper. Trophic structure analysis suggested that high sensitivity of nematode predators to intermediate levels of copper reduced predation on herbivore nematodes and resulted in greater numbers of nematodes compared to controls. p-Nitrophenol was very toxic to the nematode community, and all trophic groups were significantly reduced above 20 [mu]g g[sup [minus]1]. However, there was no effect of p-nitrophenol on microarthropods. Trinitrotoluene had no significant negative effect on total abundance of either groups of soil fauna, but oribatids were significantly reduced at 200 [mu]g g[sup [minus]1]. The results demonstrated that soil nematodes and microarthropods were sensitive indicators of environmental contaminants and that trophic-structure and community analysis has the potential to detect more subtle indirect effects of chemicals on soil food-web structure. The authors conclude that microcosms with field communities of soil microfauna offer high resolution of the ecotoxicological effects of chemicals in complex soil systems.« less

The potential of cover crops for improving soil function

NASA Astrophysics Data System (ADS)

Stoate, Chris; Crotty, Felicity

2017-04-01

Cover crops can be grown over the autumn and winter ensuring green cover throughout the year. They have been described as improving soil structure, reducing soil erosion and potentially even a form of grass weed control. These crops retain nutrients within the plant, potentially making them available for future crops, as well as increasing soil organic matter. Over the last three years, we have investigated how different cover crop regimes affect soil quality. Three separate experiments over each autumn/winter period have investigated how different cover crops affect soil biology, physics and chemistry, with each experiment building on the previous one. There have been significant effects of cover crops on soil structure, as well as significantly lower weed biomass and increased yields in the following crop - in comparison to bare stubble. For example, the effect of drilling the cover crops on soil structure in comparison to a bare stubble control that had not been driven on by machinery was quantified, and over the winter period the soil structure of the cover crop treatments changed, with compaction reduced in the cover crop treatments, whilst the bare stubble control remained unchanged. Weeds were found in significantly lower biomass in the cover crop mixes in comparison to the bare stubble control, and significantly lower weed biomass continued to be found in the following spring oat crop where the cover crops had been, indicating a weed suppressive effect that has a continued legacy in the following crop. The following spring oats have shown similar results in the last two years, with higher yields in the previous cover crop areas compared to the bare stubble controls. Overall, these results are indicating that cover crops have the potential to provide improvements to soil quality, reduce weeds and improve yields. We discuss the economic implications.

Lunar regolith and structure mechanics

NASA Technical Reports Server (NTRS)

Barnes, Frank; Ko, Hon-Yim; Sture, Stein; Carter, Tyrone R.; Evenson, Kraig A.; Nathan, Mark P.; Perkins, Steve W.

1991-01-01

The topics are presented in viewgraph form and include the following: modeling of regolith-structure interaction in extraterrestrial constructed facilities; densification of lunar soil simulant; and vibration assisted penetration of lunar soil simulant.

Bioindication in Urban Soils in Switzerland

NASA Astrophysics Data System (ADS)

Amossé, J.; Le Bayon, C.; Mitchell, E. A. D.; Gobat, J. M.

2012-04-01

Urban development leads to profound changes in ecosystem structure (e.g. biodiversity) and functioning (e.g. ecosystem services). While above-ground diversity is reasonably well studied much less is known about soil diversity, soil processes and more generally soil health in urban settings. Soil invertebrates are key actors of soil processes at different spatial and temporal scales and provide essential ecosystem services. These functions may be even more vital in stressed environments such as urban ecosystems. Despite the general recognition of the importance of soil organisms in ecosystems, soil trophic food webs are still poorly known and this is especially the case in urban settings. As urban soils are characterised by high fragmentation and stress (e.g. drought, pollution) the structure and functioning of soil communities is likely to be markedly different from that of natural soils. It is for example unclear if earthworms, whose roles in organic matter transformation and soil structuration is well documented in natural and semi-natural soils, are also widespread and active in urban soils. Bioindication is a powerful tool to assess the quality of the environment. It is complementary to classical physicochemical soil analysis or can be used as sole diagnostic tool in cases where these analyses cannot be performed. However little is known about the potential use of bioindicators in urban settings and especially it is unclear if methods developped in agriculture can be applied to urban soils. The development of reliable methods for assessing the quality of urban soils has been identified as a priority for policy making and urban management in Switzerland, a high-urbanized country. We therefore initiated a research project (Bioindication in Urban Soil - BUS). The project is organised around four parts: (i) typology of urban soils in a study Region (Neuchâtel), (ii) sampling of soil fauna and analysis of soil physicochemical properties, (iii) comparison of the functionality of urban soils and alluvial soils, used as a natural reference because of their regular physical perturbation by flooding and associated erosion/sedimentation, (iv) evaluation of soil bioindicators (e.g. earthworm, enchytraeid and testate amoebae) for urban soils. The application objective of my research is to introduce bioindicators and their limit values for the future revision of the legal Ordonnance on soils (OSol), and to develop guidelines to improve or to build urban soils with the aim of reaching a sustainable urban ecosystem development.

Spatial effects of aboveground biomass on soil ecological parameters and trace gas fluxes in a savannah ecosystem of Mount Kilimanjaro

NASA Astrophysics Data System (ADS)

Becker, Joscha; Gütlein, Adrian; Sierra Cornejo, Natalia; Kiese, Ralf; Hertel, Dietrich; Kuzyakov, Yakov

2015-04-01

The savannah biome is a hotspot for biodiversity and wildlife conservation in Africa and recently got in the focus of research on carbon sequestration. Savannah ecosystems are under strong pressure from climate and land-use change, especially around populous areas like the Mt. Kilimanjaro region. Savannah vegetation in this area consists of grassland with isolated trees and is therefore characterized by high spatial variation of canopy cover, aboveground biomass and root structure. Canopy structure is known to affect microclimate, throughfall and evapotranspiration and thereby controls soil moisture conditions. Consequently, the canopy structure is a major regulator for soil ecological parameters and soil-atmospheric trace gas exchange (CO2, N2O, CH4) in water limited environments. The spatial distribution of these parameters and the connection between above and belowground processes are important to understand and predict ecosystem changes and estimate its vulnerability. Our objective was to determine trends and changes of soil parameters and relate their spatial variability to the vegetation structure. We chose three trees from each of the two most dominant species (Acacia nilotica and Balanites aegyptiaca) in our research area. For each tree, we selected transects with nine sampling points of the same relative distances to the stem. Distances were calculated in relation to the crown radius. At these each sampling point a soil core was taken and separated in 0-10 cm and 10-30 cm depth. We measured soil carbon (C) and nitrogen (N) storage, microbial biomass carbon C and N, soil respiration as well as root biomass and -density, soil temperature and soil water content. Each tree was characterized by crown spread, leaf area index and basal area. Preliminary results show that C and N stocks decreased about 50% with depth independently of distance to the tree. Soil water content under the tree crown increased with depth while it decreased under grass cover. Microbial Biomass C and N in the upper 10 cm decreased with distance (C: r²=0.22, p<0.001; N: r²=0.3, p<0.001) as well as total soil respiration. This decrease was affected by tree size but independent from tree species. We conclude that savannah ecosystems exhibit a large spatial variability of soil parameters within the upper horizons which is strongly depend on the structure of aboveground biomass.

Wettability, soil organic matter and structure-properties of typical chernozems under the forest and under the arable land

NASA Astrophysics Data System (ADS)

Bykova, Galina; Umarova, Aminat; Tyugai, Zemfira; Milanovskiy, Evgeny; Shein, Evgeny

2017-04-01

Intensive tillage affects the properties of soil: decrease in content of soil organic matter and in hydrophobicity of the soil's solid phase, the reduction of amount of water stable aggregates - all this leads to deterioration of the structure of the soil and affects the process of movement of moisture in the soil profile. One of the hypotheses of soil's structure formation ascribes the formation of water stable aggregates with the presence of hydrophobic organic substances on the surface of the soil's solid phase. The aim of this work is to study the effect of tillage on properties of typical chernozems (pachic Voronic Chernozems, Haplic Chernozems) (Russia, Kursk region), located under the forest and under the arable land. The determination of soil-water contact angle was performed by a Drop Shape Analyzer DSA100 (Krüss GmbH, Germany) by the static sessile drop method. For all samples the content of total and organic carbon by dry combustion in oxygen flow and the particle size distribution by the laser diffraction method on the device Analysette 22 comfort, FRITCH, Germany were determined. The estimation of aggregate composition was performed by dry sieving (AS 200, Retsch, Germany), the content of water stable aggregates was estimated by the Savvinov method. There was a positive correlation between the content of organic matter and soil's wettability in studied soils, a growth of contact angle with the increasing the content of organic matter. Under the forest the content of soil organic matter was changed from 6,41% on the surface up to 1,9% at the depth of 100 cm. In the Chernozem under the arable land the organic carbon content in arable horizon is almost two times less. The maximum of hydrophobicity (78.1o) was observed at the depth of 5 cm under the forest. In the profile under the arable land the contact angle value at the same depth was 50o. The results of the structure analysis has shown a decrease in the content of agronomically valuable and water stable aggregates in the profile under arable land. These data indicate the correlation between the wettability of soils with the content of organic matter and their influence on the formation of water stable structure, as well as the negative impact of tillage on the analyzed characteristics.

Chitin amendment increases soil suppressiveness toward plant pathogens and modulates the actinobacterial and oxalobacteraceal communities in an experimental agricultural field.

PubMed

Cretoiu, Mariana Silvia; Korthals, Gerard W; Visser, Johnny H M; van Elsas, Jan Dirk

2013-09-01

A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment.

The microbial perspective of organic matter turnover and nutrient cycling in tropical soils

NASA Astrophysics Data System (ADS)

Rasche, Frank

2017-04-01

A primary goal of low-input small-holder farming systems in the tropics is the appropriate management of organic matter (OM) turnover and nutrient cycling via adapted agricultural practices. These emphasize the promotion of soil organic matter (SOM) turnover and carbon (C) sequestration, nutrient use efficiency and soil microbial activity. Since soil microbial communities are acknowledged as key players in the terrestrial C and nutrient (e.g., nitrogen (N), phosphorus (P)) cycles, they may respond sensitively to agricultural management with shifts in their community structure as well as functional traits (i.e., decomposition, mineralization). This may be in particular evident for tropical, agricultural soils which show an accelerated microbial decomposition activity induced by favourable climatic and unique physico-chemical soil conditions. While modern molecular techniques advanced primarily the understanding about the microbiome and their functional traits interacting closely with SOM dynamics in temperate soils, tropical soils under agricultural use have been still neglected to a great extent. The majority of available studies revealed mainly descriptive data on the structural composition of microbial communities rather than questioning if detected structural alterations of the soil microbiome influenced key processes in N and P cycling which actually maintain ecosystem functioning and soil productivity. This talk highlights latest efforts in deploying molecular techniques to study the compositional status of soil microbial decomposer communities and their functional attributes in response to land use change and OM management in tropical agro-ecosystems.

Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

PubMed Central

Cretoiu, Mariana Silvia; Korthals, Gerard W.; Visser, Johnny H. M.

2013-01-01

A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment. PMID:23811512

Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community.

PubMed

Wang, Yi; Li, Chunyue; Tu, Cong; Hoyt, Greg D; DeForest, Jared L; Hu, Shuijin

2017-12-31

Intensive tillage and high inputs of chemicals are frequently used in conventional agriculture management, which critically depresses soil properties and causes soil erosion and nonpoint source pollution. Conservation practices, such as no-tillage and organic farming, have potential to enhance soil health. However, the long-term impact of no-tillage and organic practices on soil microbial diversity and community structure has not been fully understood, particularly in humid, warm climate regions such as the southeast USA. We hypothesized that organic inputs will lead to greater microbial diversity and a more stable microbial community, and that the combination of no-tillage and organic inputs will maximize soil microbial diversity. We conducted a long-term experiment in the southern Appalachian mountains of North Carolina, USA to test these hypotheses. The results showed that soil microbial diversity and community structure diverged under different management regimes after long term continuous treatments. Organic input dominated the effect of management practices on soil microbial properties, although no-tillage practice also exerted significant impacts. Both no-tillage and organic inputs significantly promoted soil microbial diversity and community stability. The combination of no-tillage and organic management increased soil microbial diversity over the conventional tillage and led to a microbial community structure more similar to the one in an adjacent grassland. These results indicate that effective management through reducing tillage and increasing organic C inputs can enhance soil microbial diversity and community stability. Copyright © 2017 Elsevier B.V. All rights reserved.

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

PubMed

Su, Jian-Qiang; Ding, Long-Jun; Xue, Kai; Yao, Huai-Ying; Quensen, John; Bai, Shi-Jie; Wei, Wen-Xue; Wu, Jin-Shui; Zhou, Jizhong; Tiedje, James M; Zhu, Yong-Guan

2015-01-01

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions. © 2014 John Wiley & Sons Ltd.

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-11-01

Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane® (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.

PubMed

Liu, Peng; Jia, Shuyu; He, Xiwei; Zhang, Xuxiang; Ye, Lin

2017-12-01

Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer. Copyright © 2017 Elsevier Ltd. All rights reserved.

pH dependence and unsuitability of fluorescein dye as a tracer for pesticide mobility studies in acid soil

Treesearch

Chris Peterson

2009-01-01

The mobility of fluorescein and bromide used as tracers in packed soil columns was investigated.Five different soils were used in two application methods: soil surface application and soil incorporation, both of which simulate accepted methods of soil application of termiticides to prevent structural infestation. The...

Response of soil microbial and invertebrate communities to tracked vehicle disturbance in tallgrass prairie

Treesearch

P.S. Althoff; T.C. Todd; S.J. Thien; M.A. Callaham

2009-01-01

Soil biota drive fundamental ecosystem processes such as decomposition, nutrient cycling, and maintenance of soil structure. They are especially active in grassland ecosystems such as the tallgrass by heterotrophic soil organisms. Because both soil microbes and soil fauna display perturbation responses that integrate the physical, chemical, and biological changes to...

[Effects of rare earth elements on soil fauna community structure and their ecotoxicity to Holotrichia parallela].

PubMed

Li, Guiting; Jiang, Junqi; Chen, Jie; Zou, Yunding; Zhang, Xincai

2006-01-01

By the method of OECD filter paper contact, this paper studied the effects of applied rare earth elements on soil fauna community structure and their ecological toxicity to Holotrichia parallela in bean field. The results showed that there were no significant differences between the treatments and the control in soil fauna species, quantity of main species, and diversity index. Urgent and chronic toxic test showed that the differences between the treatments and the control were not significant. It was suggested that within the range of test dosages, rare earth elements had little ecological toxicity to Holotrichia parallela, and did not change the soil fauna community structure.

Deciphering biodegradable chelant-enhanced phytoremediation through microbes and nitrogen transformation in contaminated soils.

PubMed

Fang, Linchuan; Wang, Mengke; Cai, Lin; Cang, Long

2017-06-01

Biodegradable chelant-enhanced phytoremediation offers an alternative treatment technique for metal contaminated soils, but most studies to date have addressed on phytoextraction efficiency rather than comprehensive understanding of the interactions among plant, soil microbes, and biodegradable chelants. In the present study, we investigated the impacts of biodegradable chelants, including nitrilotriacetate, S,S-ethylenediaminedisuccinic acid (EDDS), and citric acid on soil microbes, nitrogen transformation, and metal removal from contaminated soils. The EDDS addition to soil showed the strongest ability to promote the nitrogen cycling in soil, ryegrass tissue, and microbial metabolism in comparison with other chelants. Both bacterial community-level physiological profiles and soil mass specific heat rates demonstrated that soil microbial activity was inhibited after the EDDS application (between day 2 and 10), but this effect completely vanished on day 30, indicating the revitalization of microbial activity and community structure in the soil system. The results of quantitative real-time PCR revealed that the EDDS application stimulated denitrification in soil by increasing nitrite reductase genes, especially nirS. These new findings demonstrated that the nitrogen release capacity of biodegradable chelants plays an important role in accelerating nitrogen transformation, enhancing soil microbial structure and activity, and improving phytoextraction efficiency in contaminated soil.

Combining Sequential Extractions and X-ray Absorption Spectroscopy for Quantitative and Qualitative Zinc Speciation in Soil

NASA Astrophysics Data System (ADS)

Bauer, Tatiana; Minkina, Tatiana; Batukaev, Abdulmalik; Nevidomskaya, Dina; Burachevskaya, Marina; Tsitsuashvili, Viktoriya; Urazgildieva, Kamilya

2017-04-01

The combined use of X-ray absorption spectrometry and extractive fractionation is an effective approach for studying the interaction of metal ions with soil compounds and identifying the phases-carriers of metals in soil and their stable fixation. These studies were carried out using the technique of X-ray absorption spectroscopy and chemical extractive fractionation. In a model experiment the samples taken in Calcic Chernozem were artificially contaminated with higher portion of Zn(NO3)2 (2000 mg/kg). The metal were incubated in soil samples for 2 year. The samples of soil mineral and organic phases (calcite, kaolinite, bentonite, humic acids) were saturated with Zn2+ from a solution of nitrate salts of metal. The total content of Zn in soil and soil various phases was determined using the X-ray fluorescence method. Extended X-ray absorption fine structure (EXAFS) Zn was measured at the Structural Materials Science beamline of the Kurchatov Center for Synchrotron Radiation. Sequential fractionation of Zn in soil conducted by Tessier method (Tessier et al., 1979) which determining 5 fractions of metals in soil: exchangeable, bound to Fe-Mn oxide, bound to carbonate, bound to the organic matter, and bound to silicate (residual). This methodology has so far more than 4000 citations (Web of Science), which demonstrates the popularity of this approach. Much Zn compounds are contained in uncontaminated soils in stable primary and secondary silicates inherited from the parental rocks (67% of the total concentrations in all fractions), which is a regional trait of soils in the fore-Caucasian plain. Extracted fractionation of metal compounds in soil samples, artificially contaminated with Zn salts, indicates the priority holding of Zn2+ ions by silicates, carbonates and Fe-Mn oxides. The Zn content significantly increases in the exchangeable fraction. Atomic structure study of the soil various phases saturated with Zn2+ ion by using (XANES) X-ray absorption spectroscopy allowed the determination of mechanism of metal ions interaction with soil phases and the resulting types of chemical bonds. Interaction with soil components modifies the electron structure of the metal ions themselves. The soil contamination with Zn is accompanied by decreasing the stable connection between metal and soil components. Interacting with humic acids in chernozem, the Zn2+ ion is coordinated by functional groups and ligands and forms unstable outer-sphere complexes. Zinc included into octahedral structures of layered minerals and hydro(oxides) can be inner-and outer-sphere adsorbed. The Zn2+ ions enable to replace Ca2+ ions in octahedral positions being coordinated with carbonate ions as ligands, thus forming absorbed complexes at the surface of mineral calcite. This work was supported by grant of the Russian Scientific Foundation № 16-14-10217.

Effects of low-level radioactive soil contamination and sterilization on the degradation of radiolabeled wheat straw.

PubMed

Niedrée, Bastian; Vereecken, Harry; Burauel, Peter

2012-07-01

After the explosion of reactor 4 in the nuclear power plant near Chernobyl, huge agricultural areas became contaminated with radionuclides. In this study, we want to elucidate whether (137)Cs and (90)Sr affect microorganisms and their community structure and functions in agricultural soil. For this purpose, the mineralization of radiolabeled wheat straw was examined in lab-scale microcosms. Native soils and autoclaved and reinoculated soils were incubated for 70 days at 20 °C. After incubation, the microbial community structure was compared via 16S and 18S rDNA denaturing gradient gel electrophoresis (DGGE). The radioactive contamination with (137)Cs and (90)Sr was found to have little effect on community structure and no effect on the straw mineralization. The autoclaving and reinoculation of soil had a strong influence on the mineralization and the community structure. Additionally we analyzed the effect of soil treatment on mineralization and community composition. It can be concluded that other environmental factors (such as changing content of dissolved organic carbon) are much stronger regulating factors in the mineralization of wheat straw and that low-level radiation only plays a minor role. Copyright © 2011 Elsevier Ltd. All rights reserved.

STABLE CARBON ISOTOPE RATIO AND COMPOSITION OF MICROBIAL FATTY ACIDS IN TROPICAL SOILS

EPA Science Inventory

The soil microbial community plays a critical part in tropical ecosystem functioning through its role in the soil organic matter (SOM) cycle. This study evaluates the relative effects of soil type and land use on: (1) soil microbial community structure and (2) the contribution o...

Exploring soils and ecohydrological structure in small watersheds using electromagnetic induction

USDA-ARS?s Scientific Manuscript database

Soil moisture sensors generally strive to use the real permittivity as the basis for estimating soil water content from measured electrical properties of soil. It has been shown that a reasonably good general calibration can be developed for mineral soils on this basis. However, at the low measureme...

Differences between bacterial communities in the gut of a soil-feeding termite (Cubitermes niokoloensis) and its mounds.

PubMed

Fall, Saliou; Hamelin, Jérôme; Ndiaye, Farma; Assigbetse, Komi; Aragno, Michel; Chotte, Jean Luc; Brauman, Alain

2007-08-01

In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.

Evaluation Criteria and Results of Full Scale Testing of Bridge Abutment Made from Reinforced Soil

NASA Astrophysics Data System (ADS)

Hildebrand, Maciej; Rybak, Jarosław

2017-10-01

Structures made of reinforced soil can be evaluated for their safety based on a load testing. Measurement results are essentially evaluated by displacements of surcharge (mainly in vertical direction) and facing elements (mainly in horizontal direction). Displacements are within several tenths to several millimetres and they can be taken by common geodetic equipment. Due to slow soil consolidation (progress of displacements) under constant load, observations should be made over several days or even weeks or months. A standard procedure of heating of geotextiles, used in laboratory conditions to simulate long term behaviour cannot be used in a natural scale. When the load is removed, the soil unloading occurs. Both the progress of displacements and soil unloading after unloading of the structure are the key presumptions for evaluating its safety (stability). Assessment of measuring results must be preceded by assuming even the simplest model of the structure, so as it could be possible to estimate the expected displacements under controlled load. In view of clearly random nature of soil parameters of retaining structure composed of reinforced soil and due to specific erection technology of reinforced soil structure, the assessment of its condition is largely based on expert’s judgment. It is an essential and difficult task to interpret very small displacements which are often enough disturbed by numerous factors like temperature, insolation, precipitation, vehicles, etc. In the presented paper, the authors tried to establish and juxtapose some criteria for a load test of a bridge abutment and evaluate their suitability for decision making. Final remarks are based on authors experience from a real full scale load test.

Assessment of Bacterial bph Gene in Amazonian Dark Earth and Their Adjacent Soils

PubMed Central

Brossi, Maria Julia de Lima; Mendes, Lucas William; Germano, Mariana Gomes; Lima, Amanda Barbosa; Tsai, Siu Mui

2014-01-01

Amazonian Anthrosols are known to harbour distinct and highly diverse microbial communities. As most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. To gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, composition and abundance using T-RFLP, 454-pyrosequencing and quantitative PCR essays, respectively. Soil samples were collected in two Brazilian Amazon Dark Earth (ADE) sites and at their corresponding non-anthropogenic adjacent soils (ADJ), under two different land use systems, secondary forest (SF) and manioc cultivation (M). Redundancy analysis of T-RFLP data revealed differences in bph gene structure according to both soil type and land use. Chemical properties of ADE soils, such as high organic carbon and organic matter, as well as effective cation exchange capacity and pH, were significantly correlated with the structure of bph communities. Also, the taxonomic affiliation of bph gene sequences revealed the segregation of community composition according to the soil type. Sequences at ADE sites were mostly affiliated to aromatic hydrocarbon degraders belonging to the genera Streptomyces, Sphingomonas, Rhodococcus, Mycobacterium, Conexibacter and Burkholderia. In both land use sites, shannon's diversity indices based on the bph gene data were higher in ADE than ADJ soils. Collectively, our findings provide evidence that specific properties in ADE soils shape the structure and composition of bph communities. These results provide a basis for further investigations focusing on the bio-exploration of novel enzymes with potential use in the biotechnology/biodegradation industry. PMID:24927167

Assessment of bacterial bph gene in Amazonian dark earth and their adjacent soils.

PubMed

Brossi, Maria Julia de Lima; Mendes, Lucas William; Germano, Mariana Gomes; Lima, Amanda Barbosa; Tsai, Siu Mui

2014-01-01

Amazonian Anthrosols are known to harbour distinct and highly diverse microbial communities. As most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. To gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, composition and abundance using T-RFLP, 454-pyrosequencing and quantitative PCR essays, respectively. Soil samples were collected in two Brazilian Amazon Dark Earth (ADE) sites and at their corresponding non-anthropogenic adjacent soils (ADJ), under two different land use systems, secondary forest (SF) and manioc cultivation (M). Redundancy analysis of T-RFLP data revealed differences in bph gene structure according to both soil type and land use. Chemical properties of ADE soils, such as high organic carbon and organic matter, as well as effective cation exchange capacity and pH, were significantly correlated with the structure of bph communities. Also, the taxonomic affiliation of bph gene sequences revealed the segregation of community composition according to the soil type. Sequences at ADE sites were mostly affiliated to aromatic hydrocarbon degraders belonging to the genera Streptomyces, Sphingomonas, Rhodococcus, Mycobacterium, Conexibacter and Burkholderia. In both land use sites, shannon's diversity indices based on the bph gene data were higher in ADE than ADJ soils. Collectively, our findings provide evidence that specific properties in ADE soils shape the structure and composition of bph communities. These results provide a basis for further investigations focusing on the bio-exploration of novel enzymes with potential use in the biotechnology/biodegradation industry.

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

PubMed

He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

2012-02-01

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem.

PubMed

Lee, Seung-Hoon; Kang, Hojeong

2016-02-01

The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain niche role according to biogeochemical factors, the study of the microbial community even in surface soil should be performed in detail by considering the soil depth.

Permafrost soils and carbon cycling

DOE PAGES

Ping, C. L.; Jastrow, J. D.; Jorgenson, M. T.; ...

2014-10-30

Knowledge of soils in the permafrost region has advanced immensely in recent decades, despite the remoteness and inaccessibility of most of the region and the sampling limitations posed by the severe environment. These efforts significantly increased estimates of the amount of organic carbon (OC) stored in permafrost-region soils and improved understanding of how pedogenic processes unique to permafrost environments built enormous OC stocks during the Quaternary. This knowledge has also called attention to the importance of permafrost-affected soils to the global C cycle and the potential vulnerability of the region's soil OC stocks to changing climatic conditions. In this review,more » we briefly introduce the permafrost characteristics, ice structures, and cryopedogenic processes that shape the development of permafrost-affected soils and discuss their effects on soil structures and on organic matter distributions within the soil profile. We then examine the quantity of OC stored in permafrost-region soils, as well as the characteristics, intrinsic decomposability, and potential vulnerability of this OC to permafrost thaw under a warming climate.« less

Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils.

PubMed

Lee, Seung-Hoon; Jang, Inyoung; Chae, Namyi; Choi, Taejin; Kang, Hojeong

2013-02-01

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.

Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships.

PubMed

Zhao, Jun; Zhou, Xing; Jiang, Anqi; Fan, Juanzi; Lan, Tao; Zhang, Jinbo; Cai, Zucong

2018-06-21

Soil disinfestation is an important agricultural practice to conquer soil-borne diseases and thereby ensure crop productivity. Reductive soil disinfestation (RSD) had been developed as an environmentally friendly alternative to chemical soil disinfestation (CSD). However, the differences between CSD and RSD on soil-borne pathogen suppression and fungal community structure remain poorly understood. In this work, five treatments, i.e., untreated soil (CK), CSD with 0.5 t ha -1 dazomet (DZ), RSD with 10 t ha -1 ethanol (ET), 15 t ha -1 sugarcane bagasse (SB), and 15 t ha -1 bean dregs (BD), were performed to investigate their influences on disinfestation efficiency, fungal abundance, diversity, and community structure via quantitative PCR and high-throughput sequencing. RSD-related treatments, especially the BD treatment, effectively alleviated soil acidification and salinization. The fungal abundance and microbial activity considerably increased in the BD treatment and significantly declined in the DZ treatment as compared to the CK treatment. Moreover, both CSD and RSD-related treatments significantly inhibited the population of Fusarium oxysporum and the relative abundance of genus Fusarium. Fungal community structure was notably altered by CSD and RSD practices. Furthermore, both CSD and RSD harbored a distinct unique microbiome, with the DZ treatment dominated by the genus Mortierella and BD treatment predominated by the genera Zopfiella, Chaetomium, and Penicillium. Taken together, these results indicate that the BD treatment could considerably alleviate the soil deterioration, improve soil microbial activity, and reassemble a non-pathogen unique microbiome that have more disease-suppressive agents and thus might be a promising disinfestation practice to control soil-borne disease in monoculture system.

Microbial mediated soil structure formation under wetting and drying cycles along a climate gradient (arid to humid) on hillslopes in Chile

NASA Astrophysics Data System (ADS)

Bernhard, Nadine; Moskwa, Lisa-Marie; Kühn, Peter; Mueller, Carsten W.; Wagner, Dirk; Scholten, Thomas

2017-04-01

It is well-known that the land surface resistance against erosion is largely controlled by the structure stability of the soil given by its inherent properties. Microbial activity plays a vital role in soil structure development, and thus affecting soil physical parameters. Accordingly the influence of biota shaping the earth's surface has been described through mechanisms such as mineral weathering, formation of ions and biofilms controlling land surface resistance against erosion. However the role of microorganisms for the development of soil stabilizing properties is still unclear and a precise quantitative understanding of the mechanisms under different climate conditions is widely missing. The objectives of our study are to examine to which extend microbiological processes control soil structure formation and stability and whether this is influenced by climate and topographic position. Soil samples were taken along a climate gradient and from different topographic positions of hillslopes in the Chilean Coastal Cordillera in austral autumn 2016. The variables of lithology, human disturbances and relief were held as far as possible constant whereas climate varies along the transect. We implemented 10 wet-dry cycles on air dried and sieved natural and sterile samples to enhance particle aggregation and increase structure stability. Throughout the entire experiment temperature is held constant at 20 °C to avoid changes in microbial activity. Samples are moistened and dried and each kept at the same respective pF-values for the same duration to add the same stress to each sample. Aggregate stability will be measured using wet sieving, ultrasonic dispersion and simulated rainfall. The results will be compared with on-site rainfall simulation experiments on hillslopes in the Chilean Coastal Cordillera to link laboratory results with natural field conditions. The experiment gives first insight into the aggregate formation process over time with and without microorganisms (sterilized samples). Furthermore it allows to qualify and quantify the contribution of biota to soil structure formation and stability.

Directional reflectance factors for monitoring spatial changes in soil surface structure and soil organic matter erosion in agricultural systems

NASA Astrophysics Data System (ADS)

Croft, H.; Anderson, K.

2012-04-01

Soils can experience rapid structural degradation in response to land cover changes, resulting in reduced soil productivity, increased erodibility and a loss of soil organic matter (SOM). The breakdown of soil aggregates through slaking and raindrop impact is linked to organic matter turnover, with subsequently eroded material often displaying proportionally more SOM. A reduction in aggregate stability is reflected in a decline in soil surface roughness (SSR), indicating that a soil structural change can be used to highlight soil vulnerability to SOM loss through mineralisation or erosion. Accurate, spatially-continuous measurements of SSR are therefore needed at a variety of spatial and temporal scales to understand the spatial nature of SOM erosion and deposition. Remotely-sensed data can provide a cost-effective means of monitoring changes in soil surface condition over broad spatial extents. Previous work has demonstrated the ability of directional reflectance factors to monitor soil crusting within a controlled laboratory experiment, due to changes in the levels of self-shadowing effects by soil aggregates. However, further research is needed to test this approach in situ, where other soil variables may affect measured reflectance factors and to investigate the use of directional reflectance factors for monitoring soil erosion processes. This experiment assesses the potential of using directional reflectance factors to monitor changes in SSR, aggregate stability and soil organic carbon (SOC) content for two agricultural conditions. Five soil plots representing tilled and seedbed soils were subjected to different durations of natural rainfall, producing a range of different levels of SSR. Directional reflectance factors were measured concomitantly with sampling for soil structural and biochemical tests at each soil plot. Soil samples were taken to measure aggregate stability (wet sieving), SOC (loss on ignition) and soil moisture (gravimetric method). SSM values varied from 8.70 to 20.05% and SOC from 1.33 to 1.05%, across all soil plots. Each plot was characterised using a close-range laser scanning device with a 2 mm sampling interval. The point laser data were geostatistically analysed to provide a spatially-distributed measure of SSR, giving sill variance values from 3.15 to 22.99. Reflectance factors from the soil states were measured using a ground-based hyperspectral spectroradiometer (400-2500 nm) attached to an A-frame device. This method allowed measurement at a range of viewing zenith angles from extreme forwardscatter (-60°) to extreme backscatter (+60°) at a 10° sampling resolution in the solar principal plane. Reflectance measurements were compared to geostatistically-derived indicators of SSR from the laser profile data. Forward-scattered reflectance factors exhibited a very strong relationship to SSR (R2 = 0.84 at -60°; p< 0.05), demonstrating the operational potential of directional reflectance for providing SSR measurements, despite conflicting variation in SSM. SSM also presented an interesting directional signal (R2 = 0.99 at +20°; p< 0.01). Furthermore, the results showed an important link between SRR decline as measured using directional reflectance, with a decline in aggregate stability and SOC content. These findings provide an empirical and theoretical basis for the future retrieval of spatially-continuous assessments of soil surface structure and carbon turnover within a landscape context.

Influence of biochar on the physical, chemical and retention properties of an amended sandy soil

NASA Astrophysics Data System (ADS)

Baiamonte, Giorgio; De Pasquale, Claudio; Parrino, Francesco; Crescimanno, Giuseppina

2017-04-01

Soil porosity plays an important role in soil-water retention and water availability to crops, potentially affecting both agricultural practices and environmental sustainability. The pore structure controls fluid flow and transport through the soil, as well as the relationship between the properties of individual minerals and plants. Moreover, the anthropogenic pressure on soil properties has produced numerous sites with extensive desertification process close to residential areas. Biochar (biologically derived charcoal) is produced by pyrolysis of biomasses under low oxygen conditions, and it can be applied for recycling organic waste in soils and increase soil fertility, improving soil structure and enhancing soil water storage and soil water movement. Soil application of biochar might have agricultural, environmental and sustainability advantages over the use of organic manures or compost, as it is a porous material with a high inner surface area. The main objectives of the present study were to investigate the possible application of biochar from forest residues, derived from mechanically chipped trunks and large branches of Abies alba M., Larix decidua Mill., Picea excelsa L., Pinus nigra A. and Pinus sylvestris L. pyrolysed at 450 °C for 48h, to improve soil structural and hydraulic properties (achieving a stabilization of soil). Different amount of biochar were added to a desertic sandy soil, and the effect on soil porosity water retention and water available to crops were investigated. The High Energy Moisture Characteristic (HEMC) technique was applied to investigate soil-water retention at high-pressure head levels. The adsorption and desorption isotherms of N2 on external surfaces were also determined in order to investigate micro and macro porosity ratio. Both the described model of studies on adsorption-desorption experiments with the applied isotherms model explain the increasing substrate porosity with a particular attention to the macro and micro porosity, respectively.

Soil resources and topography shape local tree community structure in tropical forests

PubMed Central

Baldeck, Claire A.; Harms, Kyle E.; Yavitt, Joseph B.; John, Robert; Turner, Benjamin L.; Valencia, Renato; Navarrete, Hugo; Davies, Stuart J.; Chuyong, George B.; Kenfack, David; Thomas, Duncan W.; Madawala, Sumedha; Gunatilleke, Nimal; Gunatilleke, Savitri; Bunyavejchewin, Sarayudh; Kiratiprayoon, Somboon; Yaacob, Adzmi; Supardi, Mohd N. Nur; Dalling, James W.

2013-01-01

Both habitat filtering and dispersal limitation influence the compositional structure of forest communities, but previous studies examining the relative contributions of these processes with variation partitioning have primarily used topography to represent the influence of the environment. Here, we bring together data on both topography and soil resource variation within eight large (24–50 ha) tropical forest plots, and use variation partitioning to decompose community compositional variation into fractions explained by spatial, soil resource and topographic variables. Both soil resources and topography account for significant and approximately equal variation in tree community composition (9–34% and 5–29%, respectively), and all environmental variables together explain 13–39% of compositional variation within a plot. A large fraction of variation (19–37%) was spatially structured, yet unexplained by the environment, suggesting an important role for dispersal processes and unmeasured environmental variables. For the majority of sites, adding soil resource variables to topography nearly doubled the inferred role of habitat filtering, accounting for variation in compositional structure that would previously have been attributable to dispersal. Our results, illustrated using a new graphical depiction of community structure within these plots, demonstrate the importance of small-scale environmental variation in shaping local community structure in diverse tropical forests around the globe. PMID:23256196

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2014 CFR

2014-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2010 CFR

2010-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2012 CFR

2012-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2013 CFR

2013-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2011 CFR

2011-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

Surface soil root response to season of repeated fire in a young longleaf pine plantation

Treesearch

Mary Anne Sword Sayer; James D. Haywood

2012-01-01

The potential exists for interaction between naturally high soil bulk density and low soil water content to create root-growth limiting soil strengths. This problem is commonly remedied by soil structural attributes, old root channels and other perturbations, and periods of wetness during which soil strength is favorable for root elongation. Because the application and...

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem.

PubMed

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-03-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem

PubMed Central

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-01-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models. PMID:26925871

Regional-scale drivers of forest structure and function in northwestern Amazonia.

PubMed

Higgins, Mark A; Asner, Gregory P; Anderson, Christopher B; Martin, Roberta E; Knapp, David E; Tupayachi, Raul; Perez, Eneas; Elespuru, Nydia; Alonso, Alfonso

2015-01-01

Field studies in Amazonia have found a relationship at continental scales between soil fertility and broad trends in forest structure and function. Little is known at regional scales, however, about how discrete patterns in forest structure or functional attributes map onto underlying edaphic or geological patterns. We collected airborne LiDAR (Light Detection and Ranging) data and VSWIR (Visible to Shortwave Infrared) imaging spectroscopy measurements over 600 km2 of northwestern Amazonian lowland forests. We also established 83 inventories of plant species composition and soil properties, distributed between two widespread geological formations. Using these data, we mapped forest structure and canopy reflectance, and compared them to patterns in plant species composition, soils, and underlying geology. We found that variations in soils and species composition explained up to 70% of variation in canopy height, and corresponded to profound changes in forest vertical profiles. We further found that soils and plant species composition explained more than 90% of the variation in canopy reflectance as measured by imaging spectroscopy, indicating edaphic and compositional control of canopy chemical properties. We last found that soils explained between 30% and 70% of the variation in gap frequency in these forests, depending on the height threshold used to define gaps. Our findings indicate that a relatively small number of edaphic and compositional variables, corresponding to underlying geology, may be responsible for variations in canopy structure and chemistry over large expanses of Amazonian forest.

Effects of bioaugmentation in para-nitrophenol-contaminated soil on the abundance and community structure of ammonia-oxidizing bacteria and archaea.

PubMed

Chi, Xiang-Qun; Liu, Kun; Zhou, Ning-Yi

2015-07-01

Pseudomonas sp. strain WBC-3 mineralizes the priority pollutant para-nitrophenol (PNP) and releases nitrite (NO2 (-)), which is probably involved in the nitrification. In this study, the rate of PNP removal in soil bioaugmented with strain WBC-3 was more accelerated with more NO2 (-) accumulation than in uninoculated soils. Strain WBC-3 survived well and remained stable throughout the entire period. Real-time polymerase chain reaction (real-time PCR) indicated a higher abundance of ammonia-oxidizing bacteria (AOB) than ammonia-oxidizing archaea (AOA), suggesting that AOB played a greater role in nitrification in the original sampled soil. Real-time PCR and multivariate analysis based on the denaturing gradient gel electrophoresis showed that PNP contamination did not significantly alter the abundance and community structure of ammonia oxidizers except for inhibiting the AOB abundance. Bioaugmentation of PNP-contaminated soil showed a significant effect on AOB populations and community structure as well as AOA populations. In addition, ammonium (NH4 (+)) variation was found to be the primary factor affecting the AOB community structure, as determined by the correlation between the community structures of ammonia oxidizers and environmental factors. It is here proposed that the balance between archaeal and bacterial ammonia oxidation could be influenced significantly by the variation in NH4 (+) levels as caused by bioaugmentation of contaminated soil by a pollutant containing nitrogen.

Demonstrations in Solute Transport Using Dyes: Part I. Procedures and Results.

ERIC Educational Resources Information Center

Butters, Greg; Bandaranayake, Wije

1993-01-01

Presents the general theory to explain chemical movement in soil. Describes classroom demonstrations with visually stimulating results that show the effects of soil structure, soil texture, soil pH, and soluble organic matter on that movement. (MDH)

[Diversity of uncultured actinomycetes in saline-alkali soil from Jiuquan area of Hexi Corridor].

PubMed

Li, Hai-yun; Niu, Shi-quan; Kong, Wei-bao; Yan, Wei-ru; Geng, Hui; Han, Cai-hong; Da, Wen-yan; Zhang, Ai-mei; Zhu, Xue-tai

2015-09-01

In order to more accurately understand community structure and diversity of actinomycetes in saline-alkali soil from Jiuquan area of Hexi Corridor, the community structure and diversity from three kinds of soil samples (primary, secondary saline alkali soil and farmland soil) were analyzed using uncultured methods. The results showed that the 16S rDNA clone library of actinomycetales from the primary saline-alkali soil belonged to 19 OTUs, Micrococcineae, Propionibacterineae, Corynebacterineae, Frankineae, Pseudonocardineae and unknown groups of Actinomycetales; the 16S r DNA clone library of actinomycetales from the secondary saline-alkali soil belonged to 14 OTUs, Micrococcineae, Propionibacterineae, Corynebacterineae, Frankineae, Pseudonocardineae and unknown groups of Actinomycetales; the 16S rDNA clone library of farmland soil belonged to 7 OTUs, Micrococcineae, Propionibacterineae, Corynebacterineae, Frankineae, Pseudonocardineae and unknown groups of Actinomycetales; Micrococcineae was the common population in the three soils, and also was the dominant population in primary saline alkali soil and farmland soil. The diversity index and rarefaction curves analysis showed that actinomycetes species richness was in order of primary saline-alkali soil > secondary saline-alkali soil > farmland soil. The dilution curves of primary saline-alkali soil and secondary saline-alkali soil were not leveled off, which indicated the actinomycetes diversity in saline-alkali soil was more enriched than the actual. The rich and diverse actinomycetes resources in saline-alkali soil from Jiuquan area of Hexi Corridor provide important data on the actinomycetes ecology distribution research, exploitation and utilization in saline-alkali soil.

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

PubMed Central

Narr, Anja; Nawaz, Ali; Wick, Lukas Y.; Harms, Hauke; Chatzinotas, Antonis

2017-01-01

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors. PMID:29067022

Spatial structure and scaling of macropores in hydrological process at small catchment scale

NASA Astrophysics Data System (ADS)

Silasari, Rasmiaditya; Broer, Martine; Blöschl, Günter

2013-04-01

During rainfall events, the formation of overland flow can occur under the circumstances of saturation excess and/or infiltration excess. These conditions are affected by the soil moisture state which represents the soil water content in micropores and macropores. Macropores act as pathway for the preferential flows and have been widely studied locally. However, very little is known about their spatial structure and conductivity of macropores and other flow characteristic at the catchment scale. This study will analyze these characteristics to better understand its importance in hydrological processes. The research will be conducted in Petzenkirchen Hydrological Open Air Laboratory (HOAL), a 64 ha catchment located 100 km west of Vienna. The land use is divided between arable land (87%), pasture (5%), forest (6%) and paved surfaces (2%). Video cameras will be installed on an agricultural field to monitor the overland flow pattern during rainfall events. A wireless soil moisture network is also installed within the monitored area. These field data will be combined to analyze the soil moisture state and the responding surface runoff occurrence. The variability of the macropores spatial structure of the observed area (field scale) then will be assessed based on the topography and soil data. Soil characteristics will be supported with laboratory experiments on soil matrix flow to obtain proper definitions of the spatial structure of macropores and its variability. A coupled physically based distributed model of surface and subsurface flow will be used to simulate the variability of macropores spatial structure and its effect on the flow behaviour. This model will be validated by simulating the observed rainfall events. Upscaling from field scale to catchment scale will be done to understand the effect of macropores variability on larger scales by applying spatial stochastic methods. The first phase in this study is the installation and monitoring configuration of video cameras and soil moisture monitoring equipment to obtain the initial data of overland flow occurrence and soil moisture state relationships.

De-icing salt contamination reduces urban tree performance in structural soil cells.

PubMed

Ordóñez-Barona, Camilo; Sabetski, Vadim; Millward, Andrew A; Steenberg, James

2018-03-01

Salts used for de-icing roads and sidewalks in northern climates can have a significant impact on water quality and vegetation. Sub-surface engineering systems, such as structural soil cells, can regulate water runoff and pollutants, and provide the necessary soil volume and irrigation to grow trees. However, the ability of such systems to manage de-icing salt contamination, and the impact of this contamination on the trees growing in them, have not been evaluated. We report on an field investigation of de-icing salt contamination in structural cells in two street-revitalization projects in Toronto, Canada, and the impact of this contamination on tree performance. We analyzed soil chemistry and collected tree attributes; these data were examined together to understand the effect of salinity on tree mortality rates and foliar condition. Data collected from continuous soil salinity loggers from April to June for one of the two sites were used to determine whether there was a long-term accumulation of salts in the soils. Results for both sites indicate that both sites displayed high salinity and alkalinity, with levels elevated beyond those suggested before those reported to cause negative tree effects. For one site, trees that were alive and trees that had a better foliar condition had significantly lower levels of soil salinity and alkalinity than other trees. High salinity and alkalinity in the soil were also associated with lower nutrient levels for both sites. Although tests for salinity accumulation in the soils of one site were negative, a longer monitoring of the soil conditions within the soil cells is warranted. Despite structural cells being increasingly utilized for their dual role in storm-water management and tree establishment, there may be a considerable trade-off between storm-water management and urban-forest function in northern climates where de-icing salt application continues to be commonplace. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synchrotron-based micro and nanotomographic investigations of soil aggregate microbial and pore structure

NASA Astrophysics Data System (ADS)

Kemner, K. M.; O'Brien, S.; Whiteside, M. D.; Sholto-Douglas, D.; Antipova, O.; Bailey, V.; Boyanov, M.; Dohnalkova, A.; Gursoy, D.; Kovarik, L.; Lai, B.; Roehrig, C.; Vogt, S.

2017-12-01

Soil is a highly complex network of pore spaces, minerals, and organic matter (e.g., roots, fungi, and bacteria), making it physically heterogeneous over nano- to macro-scales. Such complexity arises from feedbacks between physical processes and biological activity that generate a dynamic, self-organizing 3D complex. Since we first demonstrated the utility of synchrotron-based transmission tomography to image internal soil aggregate structure [Kemner et al., 1998], we and many other researchers have made use of and have advanced the application of this technique. However, our understanding of how microbes and microbial metabolism are distributed throughout soil aggregates is limited, because no technique is available to image the soil pore network and the life that inhabits it. X-ray transmission microtomography can provide highly detailed 3D renderings of soil structure but cannot distinguish cells from other electron-light material such as air or water. However, the use of CdSe quantum dots (QDs) as a reporter of bacterial presence enables us to overcome this constraint, instilling bacterial cells with enough contrast to detect them and their metabolic functions in their opaque soil habitat, with hard x-rays capable of penetrating 3D soil structures at high resolution. Previous transmission tomographic imaging of soil aggregates with high energy synchrotron x-rays has demonstrated 700 nm3 voxel spatial resolution. These and recent results from nanotomographic x-ray transmission imaging of soil aggregates with 30 nm3 voxel resolution will be presented. In addition, results of submicron voxel-sized x-ray fluorescence 3D imaging to determine microbial distributions within soil aggregates and the critical role to be played by the upgrade of the Advanced Photon Source for 100-1000X increases in hard x-ray brilliance will also be presented. *Kemner, et al., SPIE 3449, 45-53, 1998

Divergent composition but similar function of soil food webs of individual plants: plant species and community effects.

PubMed

Bezemer, T M; Fountain, M T; Barea, J M; Christensen, S; Dekker, S C; Duyts, H; van Hal, R; Harvey, J A; Hedlund, K; Maraun, M; Mikola, J; Mladenov, A G; Robin, C; de Ruiter, P C; Scheu, S; Setälä, H; Smilauer, P; van der Putten, W H

2010-10-01

Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa/groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon mineralization or food web stability. Hence, the composition and structure of entire soil food webs vary at the scale of individual plants and are strongly influenced by the species identity of the plant. However, the ecosystem functions these food webs provide are determined by the identity of the entire plant community.

Structural changes of green roof growing substrate layer studied by X-ray CT

NASA Astrophysics Data System (ADS)

Jelinkova, Vladimira; Sacha, Jan; Dohnal, Michal; Snehota, Michal

2017-04-01

Increasing interest in green infrastructure linked with newly implemented legislation/rules/laws worldwide opens up research potential for field of soil hydrology. A better understanding of function of engineered soils involved in green infrastructure solutions such as green roofs or rain garden is needed. A soil layer is considered as a highly significant component of the aforesaid systems. In comparison with a natural soil, the engineered soil is assumed to be the more challenging case due to rapid structure changes early stages after its build-up. The green infrastructure efficiency depends on the physical and chemical properties of the soil, which are, in the case of engineered soils, a function of its initial composition and subsequent soil formation processes. The project presented in this paper is focused on fundamental processes in the relatively thick layer of engineered soil. The initial structure development, during which the pore geometry is altered by the growth of plant roots, water influx, solid particles translocation and other soil formation processes, is investigated with the help of noninvasive imaging technique  X-ray computed tomography. The soil development has been studied on undisturbed soil samples taken periodically from green roof test system during early stages of its life cycle. Two approaches and sample sizes were employed. In the first approach, undisturbed samples (volume of about 63 cm3) were taken each time from the test site and scanned by X-ray CT. In the second approach, samples (volume of about 630 cm3) were permanently installed at the test site and has been repeatedly removed to perform X-ray CT imaging. CT-derived macroporosity profiles reveal significant temporal changes of soil structure. Clogging of pores by fine particles and fissures development are two most significant changes that would affect the green roof system efficiency. This work has been supported by the Ministry of Education, Youth and Sports within National Sustainability Programme I, project number LO1605 and with financial support from the Czech Science Foundation under project number GAČR 17-21011S.

The Relationship of Physical Property Indicators and Clay Soil Structural Strength of Tomsk Oblast Territory

NASA Astrophysics Data System (ADS)

Kramarenko, V. V.; Nikitenkov, A. N.; Molokov, V. Y.; Matveenko, I. A.; Shramok, A. V.

2015-11-01

The article deals with the characteristic of initial condition in fine-grained soils - its structural strength - pstr. Estimation and measurement of this factor at soil testing are of primary importance for defining its physical and mechanical properties as well as for subsequent calculation of foundation settlements that is insufficiently covered in Code of practice, national standard and inefficiently applicable in practice of engineering geological investigations. The article reveals the relationship between soil physical property, its occurrence depth, which will make possible to forecast pstr over the given territory.

Soil microbial community response to land use change in an agricultural landscape of western Kenya.

PubMed

Bossio, D A; Girvan, M S; Verchot, L; Bullimore, J; Borelli, T; Albrecht, A; Scow, K M; Ball, A S; Pretty, J N; Osborn, A M

2005-01-01

Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya. These soils have different land usage with both wooded and agricultural soils at Kakamega and Ochinga, whereas at Ochinga, Leuro, Teso, and Ugunja a replicated field experiment compared traditional continuous maize cropping against an improved N-fixing fallow system. For all sites, principal component analysis of 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles revealed that soil type was the key determinant of total bacterial community structure, with secondary variation found between wooded and agricultural soils. Similarly, phospholipid fatty acid (PLFA) analysis also separated wooded from agricultural soils, primarily on the basis of higher abundance of monounsaturated fatty acids, anteiso- and iso-branched fatty acids, and methyl-branched fatty acids in the wooded soils. At Kakamega and Ochinga wooded soils had between five 5 and 10-fold higher levels of soil carbon and microbial biomass carbon than agricultural soils from the same location, whereas total enzyme activities were also lower in the agricultural sites. Soils with woody vegetation had a lower percentage of phosphatase activity and higher cellulase and chitinase activities than the agricultural soils. BIOLOG analysis showed woodland soils to have the greatest substrate diversity. Throughout the study the two functional indicators (enzyme activity and BIOLOG), however, showed lower specificity with respect to soil type and land usage than did the compositional indicators (DGGE and PLFA). In the field experiment comparing two types of maize cropping, both the maize yields and total microbial biomass were found to increase with the fallow system. Moreover, 16S rRNA gene and PLFA analyses revealed shifts in the total microbial community in response to the different management regimes, indicating that deliberate management of soils can have considerable impact on microbial community structure and function in tropical soils.

Effects of Spatial Variability of Soil Properties on the Triggering of Rainfall-Induced Shallow Landslides

NASA Astrophysics Data System (ADS)

Fan, Linfeng; Lehmann, Peter; Or, Dani

2015-04-01

Naturally-occurring spatial variations in soil properties (e.g., soil depth, moisture, and texture) affect key hydrological processes and potentially the mechanical response of soil to hydromechanical loading (relative to the commonly-assumed uniform soil mantle). We quantified the effects of soil spatial variability on the triggering of rainfall-induced shallow landslides at the hillslope- and catchment-scales, using a physically-based landslide triggering model that considers interacting soil columns with mechanical strength thresholds (represented by the Fiber Bundle Model). The spatial variations in soil properties are represented as Gaussian random distributions and the level of variation is characterized by the coefficient of variation and correlation lengths of soil properties (i.e., soil depth, soil texture and initial water content in this study). The impacts of these spatial variations on landslide triggering characteristics were measured by comparing the times to triggering and landslide volumes for heterogeneous soil properties and homogeneous cases. Results at hillslope scale indicate that for spatial variations of an individual property (without cross correlation), the increasing of coefficient of variation introduces weak spots where mechanical damage is accelerated and leads to earlier onset of landslide triggering and smaller volumes. Increasing spatial correlation length of soil texture and initial water content also induces early landslide triggering and small released volumes due to the transition of failure mode from brittle to ductile failure. In contrast, increasing spatial correlation length of soil depth "reduces" local steepness and postpones landslide triggering. Cross-correlated soil properties generally promote landslide initiation, but depending on the internal structure of spatial distribution of each soil property, landslide triggering may be reduced. The effects of cross-correlation between initial water content and soil texture were investigated in detail at the catchment scale by incorporating correlations of both variables with topography. Results indicate that the internal structure of the spatial distribution of each soil property together with their interplays determine the overall performance of the coupled spatial variability. This study emphasizes the importance of both the randomness and spatial structure of soil properties on landslide triggering and characteristics.

Microbiomes structure and diversity in different horizons of full soil profiles

NASA Astrophysics Data System (ADS)

Chernov, Timofey; Tkhakakhova, Azida; Zhelezova, Alena; Semenov, Mikhail; Kutovaya, Olga

2017-04-01

Topsoil is a most common object for soil metagenomic studies; sometimes soil profile is being formally split in layers by depth. However, Russian Soil Science School formulated the idea of soil profile as a complex of soil horizons, which can differ in their properties and genesis. In this research we analyzed 57 genetic soil horizons of 8 different soils from European part of Russia: Albeluvisol, Greyzemic Phaeozem, three Chermozems (different land use - till, fallow, wind-protecting tree line), Rhodic Cambisol, Haplic Kastanozem and Salic Solonetz (WRB classification). Sampling was performed from all genetic horizons in each soil profile starting from topsoil until subsoil. Total DNA was extracted and 16S rRNA sequencing was provided together with chemical analysis of soil (pH measurement, C and N contents, etc.). Structure and diversity of prokaryotic community are significantly different in those soil horizons, which chemical properties and processes of origin are contrasting with nearest horizons: Na-enriched horizon of Solonetz, eluvial horizon of Albeluvisol, plough pan of Agrochernozem. Actinobacteria were abundant in top horizons of soils in warm and dry climate, while Acidobacteria had the highest frequency in soils of moist and cold regions. Concerning Archaea, Thaumarchaeota prevailed in all studied soils. Their rate was higher in microbiomes of upper horizons of steppe soils and it was reducing with depth down the profile. Prokaryotic communities in Chernozems were clustered by soil horizons types: microbiomes of A (organic topsoil) and B (mineral) horizons formed non-overlapping clusters by principal component analysis, cluster formed by prokaryotic communities of transitional soil horizons (AB) take place between clusters of A and B horizons. Moreover, prokaryotic communities of A horizons differ from each other strongly, while microbiomes of B horizons formed a narrow small cluster. It must be explaned by more diverse conditions in upper A horizons. Thus, ecological differences between soil horizons are important factor of differentiation of prokaryotic communities in soil profile; their structure can be specific for horizon type. This study was supported by Russian Science Foundation, project no. 14-26-00079

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management

USDA-ARS?s Scientific Manuscript database

Here, we demonstrate how vineyard management practices influence shifts in soil resources, which in turn affects shifts in soil-borne bacterial communities. The objective is to determine the hierarchical effects of management practices, soil attributes and location factors on the structure of soil-b...

Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage

USDA-ARS?s Scientific Manuscript database

Soil microorganisms play essential roles in soil organic matter dynamics and nutrient cycling in agroecosystems and have been used as soil quality indicators. The response of soil microbial communities to land management is complex and the long-term impacts of cropping systems on soil microbes is l...

Transformation of soil microbial community structure in response to anaerobic soil disinfestation for soil-borne disease control in strawberry

USDA-ARS?s Scientific Manuscript database

Anaerobic soil disinfestation (ASD) has been used to control soil-borne pathogens and nematodes in various plant production systems including strawberries. Disease control is commonly attributed to the depletion of oxygen and the generation of toxic compounds, including organic acids and volatiles....

Changes in the structure and function of soil ecosystems in soils contaminated with heavy metals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuperman, R.; Parmelee, R.; Carreiro, M.

1995-09-01

The structure and function of soil communities in an area with a wide range of concentrations of heavy metals was studied in portions of the U.S. Army`s Aberdeen Proving Ground, Maryland. The study included survey of soil macro- and microinvertebrate communities, soil microorganisms, enzyme activities and the rates of nutrient dynamics in soil. Soil macroinvertebrate communities showed significant reductions in the adundance of several taxonomic and functional groups in contaminated areas. The total numbers of nematodes and numbers of fungivore, bacterivore and omnivore-predator nematodes were lower in the more contaminated areas. The numbers of active bacteria and fungi were lowermore » in areas of soil contamination. Significant reduction in the activities of all enzymes closely paralleled the increase in heavy metal concentrations. Ten-to-fifty fold reductions in enzyme activities were observed as heavy metal concentrations increased. These results suggest that soil contamination with heavy metals may have detrimental effects on soil biota and the rates of organic matter degradation and subsequent release of nutrients to aboveground communities in the area.« less

Changes in the structure and function of soil ecosystems in soils contaminated with heavy metals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuperman, R.; Parmelee, R.; Carreiro, M.

1995-06-01

The structure and function of soil communities in an area with a wide range of concentrations of heavy metals was studied in portions of the U.S. Army`s Aberdeen Proving Ground, Maryland. The study included survey of soil macro- and microinvertebrate communities, soil microorganisms, enzyme activities and the rates of nutrient dynamics in soil. Soil macroinvertebrate communities showed significant reductions in the abundance of several taxonomic and functional groups in contaminated areas. The total numbers of nematodes and numbers of fungivore, bacterivore and omnivore-predator nematodes were lower in the more contaminated areas. The numbers of active bacteria and fungi were lowermore » in areas of soil contamination. Significant reduction in the activities of all enzymes closely paralleled the increase in heavy metal concentrations. Ten-to-fifty fold reductions in enzyme activities were observed as heavy metal concentrations increased. These results suggest that soil contamination with heavy metals may have detrimental effects on soil biota and the rates of organic matter degradation and subsequent release of nutrients to aboveground communities in the area.« less

Effects of spent mushroom compost application on the physicochemical properties of a degraded soil

NASA Astrophysics Data System (ADS)

Gümüş, İlknur; Şeker, Cevdet

2017-11-01

Under field and laboratory conditions, the application of organic amendments has generally shown an improvement in soil physicochemical properties. Here, spent mushroom compost (SMC) is proposed as a suitable organic amendment for soil structure restoration. Our study assessed the impact of SMC on the physicochemical properties of a weak-structured and physically degraded soil. The approach involved the establishment of a pot experiment with SMC applications into soil (control, 0.5, 1, 2, 4 and 8 %). Soils were incubated at field capacity (-33 kPa) for 21, 42, and 62 days under laboratory conditions. SMC applications into the soil significantly increased the aggregate stability (AS) and decreased the modulus of rupture. The application of SMC at rates of 1, 2, 4, and 8 % significantly increased the total nitrogen and soil organic carbon contents of the degraded soil at all incubation periods (p < 0.05). The results obtained in this study indicate that the application of SMC can improve soil physicochemical properties, which may benefit farmers, land managers, and mushroom growers.

Experimental evidence and modelling of drought induced alternative stable soil moisture states

NASA Astrophysics Data System (ADS)

Robinson, David; Jones, Scott; Lebron, Inma; Reinsch, Sabine; Dominguez, Maria; Smith, Andrew; Marshal, Miles; Emmett, Bridget

2017-04-01

The theory of alternative stable states in ecosystems is well established in ecology; however, evidence from manipulation experiments supporting the theory is limited. Developing the evidence base is important because it has profound implications for ecosystem management. Here we show evidence of the existence of alternative stable soil moisture states induced by drought in an upland wet heath. We used a long-term (15 yrs) climate change manipulation experiment with moderate sustained drought, which reduced the ability of the soil to retain soil moisture by degrading the soil structure, reducing moisture retention. Moreover, natural intense droughts superimposed themselves on the experiment, causing an unexpected additional alternative soil moisture state to develop, both for the drought manipulation and control plots; this impaired the soil from rewetting in winter. Our results show the coexistence of three stable states. Using modelling with the Hydrus 1D software package we are able to show the circumstances under which shifts in soil moisture states are likely to occur. Given the new understanding it presents a challenge of how to incorporate feedbacks, particularly related to soil structure, into soil flow and transport models?

A Novel Growing Device Inspired by Plant Root Soil Penetration Behaviors

PubMed Central

Sadeghi, Ali; Tonazzini, Alice; Popova, Liyana; Mazzolai, Barbara

2014-01-01

Moving in an unstructured environment such as soil requires approaches that are constrained by the physics of this complex medium and can ensure energy efficiency and minimize friction while exploring and searching. Among living organisms, plants are the most efficient at soil exploration, and their roots show remarkable abilities that can be exploited in artificial systems. Energy efficiency and friction reduction are assured by a growth process wherein new cells are added at the root apex by mitosis while mature cells of the root remain stationary and in contact with the soil. We propose a new concept of root-like growing robots that is inspired by these plant root features. The device penetrates soil and develops its own structure using an additive layering technique: each layer of new material is deposited adjacent to the tip of the device. This deposition produces both a motive force at the tip and a hollow tubular structure that extends to the surface of the soil and is strongly anchored to the soil. The addition of material at the tip area facilitates soil penetration by omitting peripheral friction and thus decreasing the energy consumption down to 70% comparing with penetration by pushing into the soil from the base of the penetration system. The tubular structure provides a path for delivering materials and energy to the tip of the system and for collecting information for exploratory tasks. PMID:24587244

Seismic soil structure interaction analysis for asymmetrical buildings supported on piled raft for the 2015 Nepal earthquake

NASA Astrophysics Data System (ADS)

Badry, Pallavi; Satyam, Neelima

2017-01-01

Seismic damage surveys and analyses conducted on modes of failure of structures during past earthquakes observed that the asymmetrical buildings show the most vulnerable effect throughout the course of failures (Wegner et al., 2009). Thus, all asymmetrical buildings significantly fails during the shaking events and it is really needed to focus on the accurate analysis of the building, including all possible accuracy in the analysis. Apart from superstructure geometry, the soil behavior during earthquake shaking plays a pivotal role in the building collapse (Chopra, 2012). Fixed base analysis where the soil is considered to be infinitely rigid cannot simulate the actual scenario of wave propagation during earthquakes and wave transfer mechanism in the superstructure (Wolf, 1985). This can be well explained in the soil structure interaction analysis, where the ground movement and structural movement can be considered with the equal rigor. In the present study the object oriented program has been developed in C++ to model the SSI system using the finite element methodology. In this attempt the seismic soil structure interaction analysis has been carried out for T, L and C types piled raft supported buildings in the recent 25th April 2015 Nepal earthquake (M = 7.8). The soil properties have been considered with the appropriate soil data from the Katmandu valley region. The effect of asymmetry of the building on the responses of the superstructure is compared with the author's research work. It has been studied/observed that the shape or geometry of the superstructure governs the response of the superstructure subjected to the same earthquake load.

Structure and function of methanotrophic communities in a landfill-cover soil.

PubMed

Henneberger, Ruth; Lüke, Claudia; Mosberger, Lona; Schroth, Martin H

2012-07-01

In landfill-cover soils, aerobic methane-oxidizing bacteria (MOB) convert CH(4) to CO(2), mitigating emissions of the greenhouse gas CH(4) to the atmosphere. We investigated overall MOB community structure and assessed spatial differences in MOB diversity, abundance and activity in a Swiss landfill-cover soil. Molecular cloning, terminal restriction-fragment length polymorphism (T-RFLP) and quantitative PCR of pmoA genes were applied to soil collected from 16 locations at three different depths to study MOB community structure, diversity and abundance; MOB activity was measured in the field using gas push-pull tests. The MOB community was highly diverse but dominated by Type Ia MOB, with novel pmoA sequences present. Type II MOB were detected mainly in deeper soil with lower nutrient and higher CH(4) concentrations. Substantial differences in MOB community structure were observed between one high- and one low-activity location. MOB abundance was highly variable across the site [4.0 × 10(4) to 1.1 × 10(7) (g soil dry weight)(-1)]. Potential CH(4) oxidation rates were high [1.8-58.2 mmol CH(4) (L soil air)(-1) day(-1) ] but showed significant lateral variation and were positively correlated with mean CH(4) concentrations (P < 0.01), MOB abundance (P < 0.05) and MOB diversity (weak correlation, P < 0.17). Our findings indicate that Methylosarcina and closely related MOB are key players and that MOB abundance and community structure are driving factors in CH(4) oxidation at this landfill. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

NASA Astrophysics Data System (ADS)

Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

2002-12-01

The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (P<0.05) increased in soils under cotton rotated with sorghum or wheat, and due to conservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.

Organic matter composition of soil macropore surfaces under different agricultural management practices

NASA Astrophysics Data System (ADS)

Glæsner, Nadia; Leue, Marin; Magid, Jacob; Gerke, Horst H.

2016-04-01

Understanding the heterogeneous nature of soil, i.e. properties and processes occurring specifically at local scales is essential for best managing our soil resources for agricultural production. Examination of intact soil structures in order to obtain an increased understanding of how soil systems operate from small to large scale represents a large gap within soil science research. Dissolved chemicals, nutrients and particles are transported through the disturbed plow layer of agricultural soil, where after flow through the lower soil layers occur by preferential flow via macropores. Rapid movement of water through macropores limit the contact between the preferentially moving water and the surrounding soil matrix, therefore contact and exchange of solutes in the water is largely restricted to the surface area of the macropores. Organomineral complex coated surfaces control sorption and exchange properties of solutes, as well as availability of essential nutrients to plant roots and to the preferentially flowing water. DRIFT (Diffuse Reflectance infrared Fourier Transform) Mapping has been developed to examine composition of organic matter coated macropores. In this study macropore surfaces structures will be determined for organic matter composition using DRIFT from a long-term field experiment on waste application to agricultural soil (CRUCIAL, close to Copenhagen, Denmark). Parcels with 5 treatments; accelerated household waste, accelerated sewage sludge, accelerated cattle manure, NPK and unfertilized, will be examined in order to study whether agricultural management have an impact on the organic matter composition of intact structures.

Arbuscular Mycorrhizal Fungi Community Structure, Abundance and Species Richness Changes in Soil by Different Levels of Heavy Metal and Metalloid Concentration

PubMed Central

Krishnamoorthy, Ramasamy; Kim, Chang-Gi; Subramanian, Parthiban; Kim, Ki-Yoon; Selvakumar, Gopal; Sa, Tong-Min

2015-01-01

Arbuscular Mycorrhizal Fungi (AMF) play major roles in ecosystem functioning such as carbon sequestration, nutrient cycling, and plant growth promotion. It is important to know how this ecologically important soil microbial player is affected by soil abiotic factors particularly heavy metal and metalloid (HMM). The objective of this study was to understand the impact of soil HMM concentration on AMF abundance and community structure in the contaminated sites of South Korea. Soil samples were collected from the vicinity of an abandoned smelter and the samples were subjected to three complementary methods such as spore morphology, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) for diversity analysis. Spore density was found to be significantly higher in highly contaminated soil compared to less contaminated soil. Spore morphological study revealed that Glomeraceae family was more abundant followed by Acaulosporaceae and Gigasporaceae in the vicinity of the smelter. T-RFLP and DGGE analysis confirmed the dominance of Funneliformis mosseae and Rhizophagus intraradices in all the study sites. Claroideoglomus claroideum, Funneliformis caledonium, Rhizophagus clarus and Funneliformis constrictum were found to be sensitive to high concentration of soil HMM. Richness and diversity of Glomeraceae family increased with significant increase in soil arsenic, cadmium and zinc concentrations. Our results revealed that the soil HMM has a vital impact on AMF community structure, especially with Glomeraceae family abundance, richness and diversity. PMID:26035444

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.

PubMed

Patel, Vrutika; Sharma, Anukriti; Lal, Rup; Al-Dhabi, Naif Abdullah; Madamwar, Datta

2016-03-22

Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum "Proteobacteria" and genus "Chromobacterium," respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

Visualizing the impact of living roots on rhizosphere soil structure using X-ray microtomography

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2009-04-01

The rhizosphere is an interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 μm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils.

PubMed

Long, Xi-En; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K; Zhu, Yong-Guan

2015-06-16

Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.

Bioremediation using Novosphingobium strain DY4 for 2,4-dichlorophenoxyacetic acid-contaminated soil and impact on microbial community structure.

PubMed

Dai, Yu; Li, Ningning; Zhao, Qun; Xie, Shuguang

2015-04-01

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is commonly used for weed control. The ubiquity of 2,4-D has gained increasing environmental concerns. Biodegradation is an attractive way to clean up 2,4-D in contaminated soil. However, information on the bioaugmentation trial for remediating contaminated soil is still very limited. The impact of bioaugmentation using 2,4-D-degraders on soil microbial community remains unknown. The present study investigated the bioremediation potential of a novel degrader (strain DY4) for heavily 2,4-D-polluted soil and its bioaugmentation impact on microbial community structure. The strain DY4 was classified as a Novosphingobium species within class Alphaproteobacteria and harbored 2,4-D-degrading TfdAα gene. More than 50 and 95 % of the herbicide could be dissipated in bioaugmented soil (amended with 200 mg/kg 2,4-D) respectively in 3-4 and 5-7 days after inoculation of Novosphingobium strain DY4. A significant growth of the strain DY4 was observed in bioaugmented soil with the biodegradation of 2,4-D. Moreover, herbicide application significantly altered soil bacterial community structure but bioaumentation using the strain DY4 showed a relatively weak impact.

Using semi-variogram analysis for providing spatially distributed information on soil surface condition for land surface modeling

NASA Astrophysics Data System (ADS)

Croft, Holly; Anderson, Karen; Kuhn, Nikolaus J.

2010-05-01

The ability to quantitatively and spatially assess soil surface roughness is important in geomorphology and land degradation studies. Soils can experience rapid structural degradation in response to land cover changes, resulting in increased susceptibility to erosion and a loss of Soil Organic Matter (SOM). Changes in soil surface condition can also alter sediment detachment, transport and deposition processes, infiltration rates and surface runoff characteristics. Deriving spatially distributed quantitative information on soil surface condition for inclusion in hydrological and soil erosion models is therefore paramount. However, due to the time and resources involved in using traditional field sampling techniques, there is a lack of spatially distributed information on soil surface condition. Laser techniques can provide data for a rapid three dimensional representation of the soil surface at a fine spatial resolution. This provides the ability to capture changes at the soil surface associated with aggregate breakdown, flow routing, erosion and sediment re-distribution. Semi-variogram analysis of the laser data can be used to represent spatial dependence within the dataset; providing information about the spatial character of soil surface structure. This experiment details the ability of semi-variogram analysis to spatially describe changes in soil surface condition. Soil for three soil types (silt, silt loam and silty clay) was sieved to produce aggregates between 1 mm and 16 mm in size and placed evenly in sample trays (25 x 20 x 2 cm). Soil samples for each soil type were exposed to five different durations of artificial rainfall, to produce progressively structurally degraded soil states. A calibrated laser profiling instrument was used to measure surface roughness over a central 10 x 10 cm plot of each soil state, at 2 mm sample spacing. The laser data were analysed within a geostatistical framework, where semi-variogram analysis quantitatively represented the change in soil surface structure during crusting. The laser data were also used to create digital surface models (DSM) of the soil states for visual comparison. This research has shown that aggregate breakdown and soil crusting can be shown quantitatively by a decrease in sill variance (silt soil: 11.67 (control) to 1.08 (after 90 mins rainfall)). Features present within semi-variograms were spatially linked to features at the soil surface, such as soil cracks, tillage lines and areas of deposition. Directional semi-variograms were used to provide a spatially orientated component, where the directional sill variance associated with a soil crack was shown to increase from 7.95 to 19.33. Periodicity within semi-variogram was also shown to quantify the spatial scale of soil cracking networks and potentially surface flowpaths; an average distance between soil cracks of 37 mm closely corresponded to the distance of 38 mm shown in the semi-variogram. The results provide a strong basis for the future retrieval of spatio-temporal variations in soil surface condition. Furthermore, the presence of process-based information on hydrological pathways within semi-variograms may work towards an inclusion of geostatisically-derived information in land surface models and the understanding of complex surface processes at different spatial scales.

A simple procedure for estimating soil porosity

NASA Astrophysics Data System (ADS)

Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Holden, Nick

2016-04-01

Soil degradation from mismanagement is of international concern. Simple, accessible tools for rapidly assessing impacts of soil management are required. Soil structure is a key component of soil quality and porosity is a useful indicator of structure. We outline a version of a procedure described by Piwowarczyk et al. (2011) used to estimate porosity of samples taken during a soil quality survey of 38 sites across Ireland as part of the Government funded SQUARE (Soil Quality Assessment Research) project. This required intact core (r = 2.5 cm, H = 5cm) samples taken at 5-10 cm and 10-20 cm depth, to be covered with muslin cloth at one end and secured with a jubilee clip. Samples were saturated in sealable water tanks for ≈ 64 hours, then allowed to drain by gravity for 24 hours, at which point Field Capacity (F.C.) was assumed to have been reached, followed by oven drying with weight determined at each stage. This allowed the calculation of bulk density and the estimation of water content at saturation and following gravitational drainage, thus total and functional porosity. The assumption that F.C. was reached following 24 hours of gravitational drainage was based on the Soil Moisture Deficit model used in Ireland to predict when soils are potentially vulnerable to structural damage and used nationally as a management tool. Preliminary results indicate moderately strong, negative correlations between estimated total porosity at 5-10 cm and 10-20 cm depth (rs = -0.7, P < 0.01 in both cases) and soil quality scores of the Visual Evaluation of Soil Structure (VESS) method which was conducted at each survey site. Estimated functional porosity at 5-10 cm depth was found to moderately, negatively correlate with VESS scores (rs = - 0.5, P < 0.05). This simple procedure requires inexpensive equipment and appears useful in indicating porosity of a large quantity of samples taken at numerous sites or if done periodically, temporal changes in porosity at a field scale, indicating the impacts of soil management. Reference Piwowarczyk, A., Giuliani, G. & Holden, N.M. 2011. Can soil moisture deficit be used to forecast when soils are at high risk of damage owing to grazing animals? Soil Use and Management, 27, 255-263.

Identification and classification of structural soil conservation measures based on very high resolution stereo satellite data.

PubMed

Eckert, Sandra; Tesfay Ghebremicael, Selamawit; Hurni, Hans; Kohler, Thomas

2017-05-15

Land degradation affects large areas of land around the globe, with grave consequences for those living off the land. Major efforts are being made to implement soil and water conservation measures that counteract soil erosion and help secure vital ecosystem services. However, where and to what extent such measures have been implemented is often not well documented. Knowledge about this could help to identify areas where soil and water conservation measures are successfully supporting sustainable land management, as well as areas requiring urgent rehabilitation of conservation structures such as terraces and bunds. This study explores the potential of the latest satellite-based remote sensing technology for use in assessing and monitoring the extent of existing soil and water conservation structures. We used a set of very high resolution stereo Geoeye-1 satellite data, from which we derived a detailed digital surface model as well as a set of other spectral, terrain, texture, and filtered information layers. We developed and applied an object-based classification approach, working on two segmentation levels. On the coarser level, the aim was to delimit certain landscape zones. Information about these landscape zones is useful in distinguishing different types of soil and water conservation structures, as each zone contains certain specific types of structures. On the finer level, the goal was to extract and identify different types of linear soil and water conservation structures. The classification rules were based mainly on spectral, textural, shape, and topographic properties, and included object relationships. This approach enabled us to identify and separate from other classes the majority (78.5%) of terraces and bunds, as well as most hillside terraces (81.25%). Omission and commission errors are similar to those obtained by the few existing studies focusing on the same research objective but using different types of remotely sensed data. Based on our results, we estimate that the construction of the conservation structures in our study area in Eritrea required over 300,000 person-days of work, which underlines the huge efforts involved in soil and water conservation. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Characteristics of soil macrofaunal community structure in secondary forest and forest plantations in western Qinling Mountains of Northwest China].

PubMed

Liu, Ji-Liang; Cao, Jing; Li, Shi-Jie; Pan, Chun-Lin; Pan, Cheng-Chen

2012-09-01

Long-term disturbance of human beings on secondary forest ecosystem would have profound impacts on belowground ecological processes, whereas the community structure and functional diversity of soil fauna would be sensitive to the changes of belowground ecological processes, with significance as an indicator of the changes. In this study, the method of hand-sorting was adopted to investigate the density of soil macrofaunal community in a secondary forest and the Pinus tabulaeformis, Larix kaempferi, Picea abie, and Picea asperata plantations of nearly 30 years old in Xiaolongshan forest area of western Qinling Mountains, and the PCA ordination and one-way ANOVA analysis were applied to analyze the community structure and trophic group composition of soil macrofauna in the five forest types. In the P. tabulaeformis and L. kaempferi plantations, the density of soil macrofaunal community was 3.0 and 2.1 times of that in the secondary forest, respectively, and the consumers/decomposers ratio of the community was obviously higher than that in the secondary forest. Among the plantations, P. tabulaeformis and L. kaempferi plantations had a significantly higher consumers/decomposers ratio of soil macrofaunal community than P. abies and P. asperata plantations. There was an obvious difference in community structure of soil macrofauna among the four plantations. The density of soil macrofaunal community in P. tabulaeformis and L. kaempferi plantations was 3.5 and 2.1 times higher than that in P. asperata plantation, respectively, whereas the group richness of soil macrofaunal community in P. tabulaeformis plantation was 1.5 times of that in P. abies and P. asperata plantations.

Community structure and elevational diversity patterns of soil Acidobacteria.

PubMed

Zhang, Yuguang; Cong, Jing; Lu, Hui; Li, Guangliang; Qu, Yuanyuan; Su, Xiujiang; Zhou, Jizhong; Li, Diqiang

2014-08-01

Acidobacteria is one of the most dominant and abundant phyla in soil, and was believed to have a wide range of metabolic and genetic functions. Relatively little is known about its community structure and elevational diversity patterns. We selected four elevation gradients from 1000 to 2800 m with typical vegetation types of the northern slope of Shennongjia Mountain in central China. The vegetation types were evergreen broadleaved forest, deciduous broadleaved forest, coniferous forest and sub-alpine shrubs. We analyzed the soil acidobacterial community composition, elevational patterns and the relationship between Acidobacteria subdivisions and soil enzyme activities by using the 16S rRNA meta-sequencing technique and multivariate statistical analysis. The result found that 19 known subdivisions as well as an unclassified phylotype were presented in these forest sites, and Subdivision 6 has the highest number of detectable operational taxonomic units (OTUs). A significant single peak distribution pattern (P<0.05) between the OTU number and the elevation was observed. The Jaccard and Bray-Curtis index analysis showed that the soil Acidobacteria compositional similarity significantly decreased (P<0.01) with the increase in elevation distance. Mantel test analysis showed the most of the soil Acidobacteria subdivisions had the significant relationship (P<0.01) with different soil enzymes. Therefore, soil Acidobacteria may be involved in different ecosystem functions in global elemental cycles. Partial Mantel tests and CCA analysis showed that soil pH, soil temperature and plant diversity may be the key factors in shaping the soil Acidobacterial community structure. Copyright © 2014. Published by Elsevier B.V.

CO2 efflux from soil under influence of cadmium and glucose

NASA Astrophysics Data System (ADS)

Gilmullina, Aliia; Galitskaya, Polina; Selivanovskaya, Svetlana

2017-04-01

Soil is the largest pool of organic carbon. Any anthropogenic activity may change the soil organic carbon stock resulting in the atmospheric carbon concentration increase. Organic wastes and sewage sludge are often used for soil fertilization. These amendments often contain not only organic compounds stimulating soil microflora but also toxic compounds e.g. metals inhibiting them. The question about the influence of such amendments on soil carbon stock still remains open. The aim of this study was to evaluate individual glucose and cadmium (Cd) additions and their combined effects on carbon mineralization and microbial community structure in forest soil sampled from different depths (0-20 cm, 20-40 cm and 40-60 cm). We incubated soil samples for 14 days after the addition of: glucose (10000 mg kg-1), Cd (300 mg kg-1) and their mixture. CO2 efflux was measured by CO2 trapping in NaOH, at the 3rd, 7th and 14th days of incubation DNA was extracted from soil samples for assessment of microbial community structure via real-time PCR and Illumina sequencing. Glucose addition induced the increase of soil respiration and fungal-bacterial ratio. However, bacterial alpha-biodiversity decreased as glucose addition caused the dominance of Proteobacteria (0-20 cm, 20-40 cm and 40-60 cm), Actinobacteria (20-40 cm) and Acidobacteria (40-60 cm) phyla. Single Cd addition did not have any effect on parameters studied. In case of simultaneous addition of glucose and Cd, soil respiration and microbial community structure mainly depended more on glucose amendment as compared with metal.

Visualization of soil particulate organic matter by means of X-ray CT?

NASA Astrophysics Data System (ADS)

Sleutel, Steven; Van Loo, Denis; Maenhout, Peter; Van Hoorebeke, Luc; Cnudde, Veerle; De Neve, Stefaan

2014-05-01

The role of soil structure in organic matter (OM) stabilization has been primarily investigated through physical fractionation studies operative at the scale of aggregates and smaller organo-mineral particles. By narrowing down soil structure to an arrangement of mineral and organic particles, the majority of studies did not explore the spatial organization of the soil pore network, the actual habitat of microorganisms. The pore structure of soil can have a significant impact on soil processes like OM decomposition by excluding OM from micro-organisms in small pores, by regulating the diffusion of substrates and metabolites and by regulating aeration and presence of moisture. Because of its ability to visualize the 3D architecture of soil non-destructively, X-ray Computed Tomography (CT) is becoming a widespread tool for studying soil pore network structure. However, phase determination of pore space, soil OM, soil mineral matter (MM) and water is often limited even with the latest technological and software advances, allowing high resolution and better quality imaging. Contrast agents commonly used in histology enable enhancement of X-ray attenuation of targeted structures or compounds. Here we report on the first systematic investigation of the use of such X-ray contrast agents for soil research. An evaluation procedure as well as a method to apply the agents to soil samples was developed and applied on reference soil samples. The effectiveness and selectivity of the contrast agents was evaluated for soil organic matter (SOM), MM and water. Several products were found to selectively increase the attenuation of water or SOM. The four agents with the best OM-staining capabilities (Phosphomolybdenic acid (PMA), silver nitrate, lead nitrate and lead acetate) were further tested on an OM-MM mixture. Observed differences in reactivity of the staining agents with MM components were apparent, suggesting that contrasting agents may have to be selected for the specific composition of the soil mineral matrix. Furthermore, techniques such as multiple-energy scanning and K-edge imaging, even in the future perhaps in combination with spectral resolving detectors or spectroscopic techniques can could further enhance the potential benefit from this study of X-ray CT staining agents. The high Z elements of the staining agents have unique and characteristic traits that can be detected or quantified with the abovementioned techniques and methods. We conclude that, given resolution limits and inherent presence of partial volume effects staining, X-ray CT-based localization of discrete SOM particles will be limited to a lower limit of 20-50 µm. Still, the improved 3D visualization of OM and soil pore space opens up possibilities for tailored lab experiments with measures of microbial activity, which could generate new insights in carbon cycling at small scales. In addition, we report on a lab incubation experiment in which CO2 respiration from soil cores was monitored (headspace GC analysis) and an X-ray CT approach yielded soil pore size distributions. We incubated a sandy loam soil (with application of ground grass or sawdust) in 18 small aluminium rings (Ø 1 cm, h 1 cm). Bulk density was adjusted to 1.1 or 1.3 Mg m-3 (compaction) and 6 rings were filled at a coarser Coarse Sand:Fine Sand:Silt+Clay ratio. While compaction induced a strong reduction in the cumulative C mineralization for both grass and sawdust substrates, artificial change to a coarser soil texture only reduced net C mineralization from the added sawdust. There thus appears to be a strong interaction effect between soil pore structure and substrate type on substrate decomposition. Correlation coefficients between the C mineralization rates and volumes of 7 pore size classes (from the X-ray CT data) also showed an increasing positive correlation with increasing pore size. Since any particulate organic matter initially present in the soil was removed prior to the experiment (sieving, ashing the >53µm fraction and recombining with the <53µm fraction), the added OM can be localized by means of X-ray CT. Through on-going image analysis the surrounding porosity of the added grass or sawdust particles is being quantified to further study the interaction between the soil pore structure and substrate decomposition.

Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

PubMed Central

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes. PMID:25909444

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

DOE PAGES

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; ...

2015-07-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.« less

Fractal Feature of Particle-Size Distribution in the Rhizospheres and Bulk Soils during Natural Recovery on the Loess Plateau, China

PubMed Central

Song, Zilin; Zhang, Chao; Liu, Guobin; Qu, Dong; Xue, Sha

2015-01-01

The application of fractal geometry to describe soil structure is an increasingly useful tool for better understanding the performance of soil systems. Only a few studies, however, have focused on the structure of rhizospheric zones, where energy flow and nutrient recycling most frequently occur. We used fractal dimensions to investigate the characteristics of particle-size distribution (PSD) in the rhizospheres and bulk soils of six croplands abandoned for 1, 5, 10, 15, 20, and 30 years on the Loess Plateau of China and evaluated the changes over successional time. The PSDs of the rhizospheres and the fractal dimensions between rhizosphere soil and bulk soils during the natural succession differed significantly due to the influence of plant roots. The rhizospheres had higher sand (0.05–1.00 mm) contents, lower silt (<0.002 mm) contents, and lower fractal dimensions than the bulk soils during the early and intermediate successional stages (1–15 years). The fractal dimensions of the rhizosphere soil and bulk soil ranged from 2.102 to 2.441 and from 2.214 to 2.459, respectively, during the 30-year restoration. Rhizospheric clay and silt contents and fractal dimension tended to be higher and sand content tended to be lower as abandonment age increased, but the bulk soils had the opposite trend. Linear regression analysis indicated that the fractal dimensions of both the rhizospheres and bulk soils were significantly linearly correlated with clay, sand, organic-carbon, and total-nitrogen contents, with R 2 ranging from 0.526 to 0.752 (P<0.001). In conclusion, PSD differed significantly between the rhizosphere soil and bulk soil. The fractal dimension was a sensitive and useful index for quantifying changes in the properties of the different soil zones. This study will greatly aid the application of the fractal method for describing soil structure and nutrient status and the understanding of the performance of rhizospheric zones during ecological restoration. PMID:26368339

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

PubMed

Negassa, Wakene C; Guber, Andrey K; Kravchenko, Alexandra N; Marsh, Terence L; Hildebrandt, Britton; Rivers, Mark L

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.« less

Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.

PubMed

Song, He; Che, Zhao; Cao, Wenchao; Huang, Ting; Wang, Jingguo; Dong, Zhaorong

2016-06-01

Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.

Experimental evidence of the role of pores on movement and distribution of bacteria in soil

NASA Astrophysics Data System (ADS)

Kravchenko, Alexandra N.; Rose, Joan B.; Marsh, Terence L.; Guber, Andrey K.

2014-05-01

It has been generally recognized that micro-scale heterogeneity in soil environments can have a substantial effect on movement, fate, and survival of soil microorganisms. However, only recently the development of tools for micro-scale soil analyses, including X-ray computed micro-tomography (μ-CT), enabled quantitative analyses of these effects. The long-term goal of our work is to explore how differences in micro-scale characteristics of pore structures influence movement, spatial distribution patterns, and activities of soil microorganisms. Using X-ray μ-CT we found that differences in land use and management practices lead to development of contrasting patterns in pore size-distributions within intact soil aggregates. Then our experiments with Escherichia coli added to intact soil aggregates demonstrated that the differences in pore structures can lead to substantial differences in bacteria redistribution and movement within the aggregates. Specifically, we observed more uniform E.coli redistribution in aggregates with homogeneously spread pores, while heterogeneous pore structures resulted in heterogeneous E.coli patterns. Water flow driven by capillary forces through intact aggregate pores appeared to be the main contributor to the movement patterns of the introduced bacteria. Influence of pore structure on E.coli distribution within the aggregates further continued after the aggregates were subjected to saturated water flow. E. coli's resumed movement with saturated water flow and subsequent redistribution within the soil matrix was influenced by porosity, abundance of medium and large pores, pore tortuosity, and flow rates, indicating that greater flow accompanied by less convoluted pores facilitated E. coli transport within the intra-aggregate space. We also found that intra-aggregate heterogeneity of pore structures can have an effect on spatial distribution patterns of indigenous microbial populations. Preliminary analysis showed that in aggregates from an organic agricultural system with cover crops, characterized by greater intra-aggregate pore heterogeneity, bacteria of Actinobacteria and Firmicutes groups were more abundant in presence of large as compared to small pores. In contrast, no differences were observed in the aggregates from conventionally managed soil, overall characterized by homogeneous intra-aggregate pore patterns. Further research efforts are being directed towards quantification of the pore structure effects on activities and community composition of soil microorganisms.

Land use Effects on Storage, Stability and Structure of Organic Carbon in Soil Density Fractions Revealed by 13C Natural Abundance and CPMAS 13C NMR

NASA Astrophysics Data System (ADS)

Flessa, H.; Helfrich, M.; John, B.; Yamashita, T.; Ludwig, B.

2004-12-01

The type of land use and soil cultivation are important factors controlling organic carbon storage (SOC) in soils and they can also influence the relative importance, the structure, and the stability of different SOC pools. The objectives of our study were: i) to quantify the SOC stocks in different density fractions (mineral-associated soil organic matter > 2 g cm-3 (Mineral-SOM), free particulate organic matter < 1.6 g cm-3 (free POM), light occluded particulate organic matter < 1.6 g cm-3 (occluded POM<1.6) and dense occluded particulate organic matter 1.6 to 2.0 g cm-3 (occluded POM1.6-2.0)) of silty soils under different land use (spruce forest, grassland, maize, wheat), ii) to determine the structure of these SOC fractions by CPMAS 13C NMR spectroscopy, and iii) to analyse the stability of these SOC fractions in the maize soil on the basis of the stable isotope composition of SOC. The SOC concentration in the A horizon increased in the order wheat (12.7 g kg-1) < maize (13.0 g kg-1) < grassland (24.5 g kg-1) < spruce (40.5 g kg-1). The major part (86-91%) of the SOC was associated with the heavy mineral fraction at the grassland, maize and wheat site. In the A horizon of the spruce soil, the particulate organic matter accounted for 52% of the total SOC content. The chemical structure of the soil organic matter (SOM) was influenced by litter quality, the intensity of litter decomposition and the related production and storage of microbially-derived substances. SOM of the acid forest soil was characterized by large amounts of POM with a high content of spruce litter-derived alkyl C. In the biologically more active grassland and maize soil, litter-derived POM was decomposed more rapidly and SOC stocks were dominated by mineral-associated SOM which contained greater proportions of aryl and carbonyl C. The cultivation of the grassland soil induced enhanced mineralization of POM and in particular of mineral-associated SOM. The faster SOC turnover was associated with a relative accumulation of aromatic and carbonyl C structures in the mineral-bound SOM. In all soils, the free particulate organic matter had a smaller proportion of alkyl C and a larger proportion of O-alkyl C than the particulate organic matter occluded in aggregates. The mean age of the SOM in the density fractions of the maize soil increased with increasing aromaticity in the order free POM (22 yr) < occluded POM1.6-2.0 (49 yr) < mineral-associated SOM (63 yr). The results showed that the type of land use influenced the distribution pattern of litter carbon to functionally different SOM pools which represented different stages of SOM decomposition and humification. Additionally, the type of land use influenced the chemical structure of SOM in soil density fractions. Thus, the effect of land use on SOM storage should not only be assessed in terms of total C stocks but also with respect to changes of SOC structure, stability and function.

Clay:organic-carbon and organic carbon as determinants of the soil physical properties: reassessment of the Complexed Organic Carbon concept

NASA Astrophysics Data System (ADS)

Matter, Adrien; Johannes, Alice; Boivin, Pascal

2016-04-01

Soil Organic Carbon (SOC) is well known to largely determine the soil physical properties and fertility. Total porosity, structural porosity, aeration, structural stability among others are reported to increase linearly with increasing SOC in most studies. Is there an optimal SOC content as target in soil management, or is there no limit in physical fertility improvement with SOC? Dexter et al. (2008) investigated the relation between clay:SOC ratio and the physical properties of soils from different databases. They observed that the R2 of the relation between SOC and the physical properties were maximized when considering the SOC fraction limited to a clay:SOC ratio of 10. They concluded that this fraction of the SOC was complexed, and that the additional SOC was not influencing the physical properties as strongly as the complexed one. In this study, we reassessed this approach, on a database of 180 undisturbed soil samples collected from cambiluvisols of the Swiss Plateau, on an area of 2400 km2, and from different soil uses. The physical properties were obtained with Shrinkage Analysis, which involved the parameters used in Dexter et al., 2008. We used the same method, but detected biases in the statistical approach, which was, therefore, adapted. We showed that the relation between the bulk density and SOC was changing with the score of visual evaluation of the structure (VESS) (Ball et al., 2007). Therefore, we also worked only on the "good" structures according to VESS. All shrinkage parameters were linearly correlated to SOC regardless of the clay:SOC ratio, with R2 ranging from 0.45 to 0.8. Contrarily to Dexter et al. (2008), we did not observed an optimum in the R2 of the relation when considering a SOC fraction based on the clay:SOC ratio. R2 was increasing until a Clay:SOC of about 7, where it reached, and kept, its maximum value. The land use factor was not significant. The major difference with the former study is that we worked on the same soil group, on a large range of texture, with less sandy soils and accounting for structural state. Our results show that, on this soil group, any SOC increase almost linearly increases the physical properties and, therefore, the physical fertility and the ecological functions of the soil, regardless of the clay:SOC ratio. When considering the whole SOC instead of a fraction, we show that the 10 clay:SOC ratio, however corresponds to a good structure according to VESS and optimal physical values. Therefore, we think reaching a clay:SOC ratio of 10 must be considered as an objective for farmers and advisers. Ball, B.C., T. Batey, and L.J. Munkholm. 2007. Field assessment of soil structural quality - a development of the Peerlkamp test. Soil Use Manag. 23(4): 329-337. Dexter, A.R., G. Richard, D. Arrouays, E.A. Czyz, C. Jolivet, and O. Duval. 2008. Complexed organic matter controls soil physical properties. Geoderma 144(3-4): 620-627.

Soil microbial community profiles and functional diversity in limestone cedar glades

USGS Publications Warehouse

Cartwright, Jennifer M.; Dzantor, E. Kudjo; Momen, Bahram

2016-01-01

Rock outcrop ecosystems, such as limestone cedar glades (LCGs), are known for their rare and endemic plant species adapted to high levels of abiotic stress. Soils in LCGs are thin (< 25 cm), soil-moisture conditions fluctuate seasonally between xeric and saturated, and summer soil temperatures commonly exceed 48 °C. The effects of these stressors on soil microbial communities (SMC) remain largely unstudied, despite the importance of SMC-plant interactions in regulating the structure and function of terrestrial ecosystems. SMC profiles and functional diversity were characterized in LCGs using community level physiological profiling (CLPP) and plate-dilution frequency assays (PDFA). Most-probable number (MPN) estimates and microbial substrate-utilization diversity (H) were positively related to soil thickness, soil organic matter (OM), soil water content, and vegetation density, and were diminished in alkaline soil relative to circumneutral soil. Soil nitrate showed no relationship to SMCs, suggesting lack of N-limitation. Canonical correlation analysis indicated strong correlations between microbial CLPP patterns and several physical and chemical properties of soil, primarily temperature at the ground surface and at 4-cm depth, and secondarily soil-water content, enabling differentiation by season. Thus, it was demonstrated that several well-described abiotic determinants of plant community structure in this ecosystem are also reflected in SMC profiles.

Visualization of physico-chemical properties and microbial distribution in soil and root microenvironments

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2016-04-01

Plant root development is influenced by soil properties and environmental factors. In turn plant roots can also change the physico-chemical conditions in soil resulting in gradients between roots and the root-free bulk soil. By releasing a variety of substances roots facilitate microbial activities in their direct vicinity, the rhizosphere. The related microorganisms are relevant for various ecosystem functions in the root-soil interface such as nutrient cycling. It is therefore important to study the impact and dynamics of microorganisms associated to different compartments in root-soil interfaces on a biologically meaningful micro-scale. The analysis of microorganisms in their habitats requires microscopic observations of the respective microenvironment. This can be obtained by preserving the complex soil structure including the root system by resin impregnation resulting in high quality thin sections. The observation of such sections via fluorescence microscopy, SEM-EDS, and Nano-SIMS will be highlighted in this presentation. In addition, we will discuss the combination of this methodological approach with other imaging techniques such as planar optodes or non-invasive 3D X-ray CT to reveal the entire spatial structure and arrangement of soil particles and roots. When combining the preservation of soil structure via resin impregnation with 16S rRNA targeted fluorescence in situ hybridization (FISH) single microbial cells can be visualized, localized, and quantified in the undisturbed soil matrix including the root-soil interfaces. The simultaneous use of multiple oligonucleotide probes thereby provides information on the spatial distribution of microorganisms belonging to different phylogenetic groups. Results will be shown for paddy soils, where management induced physico-chemical dynamics (flooding and drying) as well as resulting microbial dynamics were visualized via correlative microscopy in resin impregnated samples.

Greatest soil microbial diversity found in micro-habitats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bach, Elizabeth M.; Williams, Ryan J.; Hargreaves, Sarah K.

Microbial interactions occur in habitats much smaller than typically considered in classic ecological studies. This study uses soil aggregates to examine soil microbial community composition and structure of both bacteria and fungi at a microbially relevant scale. Aggregates were isolated from three land management systems in central Iowa, USA to test if aggregate-level microbial responses were sensitive to large-scale shifts in plant community and management practices. Bacteria and fungi exhibited similar patterns of community structure and diversity among soil aggregates, regardless of land management. Microaggregates supported more diverse microbial communities, both taxonomically and functionally. Calculation of a weighted proportional wholemore » soil diversity, which accounted for microbes found in aggregate fractions, resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil. Our results show microaggregates support a previously unrecognized diverse microbial community that likely effects microbial access and metabolism of soil substrates.« less

Microbial activities related to C and N cycling and microbial community structure in the rhizospheres of Pinus sylvestris, Picea abies and Betula pendula seedlings in an organic and mineral soil.

PubMed

Priha; Grayston; Pennanen; Smolander

1999-10-01

The aim of this study was to determine whether Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies (L.) Karst.) and silver birch (Betula pendula Roth) seedlings have a selective influence on the soil microbial community structure and activity and whether this varies in different soils. Seedlings of pine, spruce and birch were planted into pots of two soil types: an organic soil and a mineral soil. Pots without seedlings were also included. After one growing season, microbial biomass C (C(mic)) and N (N(mic)), C mineralization, net ammonification, net nitrification, denitrification potential, phospholipid fatty acid (PLFA) patterns and community level physiological profiles (CLPPs) were measured in the rhizosphere soil of the seedlings. In the organic soil, C(mic) and N(mic) were higher in the birch rhizosphere than in pine and spruce rhizosphere. The C mineralization rate was not affected by tree species. Unplanted soil contained the highest amount of mineral N and birch rhizosphere the lowest, but rates of net N mineralization and net nitrification did not differ between treatments. The microbial community structure, measured by PLFAs, had changed in the rhizospheres of all tree species compared to the unplanted soil. Birch rhizosphere was most clearly separated from the others. There was more of the fungal specific fatty acid 18:2omega6,9 and more branched fatty acids, common in Gram-positive bacteria, in this soil. CLPPs, done with Biolog GN plates and 30 additional substrates, separated only birch rhizosphere from the others. In the mineral soil, roots of all tree species stimulated C mineralization in soil and prevented nitrification, but did not affect C(mic) and N(mic), PLFA patterns or CLPPs. The effects of different tree species did not vary in the mineral soil. Thus, in the mineral soil, the strongest effect on soil microbes was the presence of a plant, regardless of the tree species, but in the organic soil, different tree species varied in their influence on soil microbes.

Assessment of the content, structure, and source of soil dissolved organic matter in the coastal wetlands of Jiaozhou Bay, China

NASA Astrophysics Data System (ADS)

Xi, Min; Zi, Yuanyuan; Wang, Qinggai; Wang, Sen; Cui, Guolu; Kong, Fanlong

2018-02-01

The contents and the spectral analysis of dissolved organic matter (DOM) in four typical wetlands, such as naked tidal, suaeda salsa, reed and spartina, were conducted to investigate the content, structure, and source of DOM in coastal wetland soil. The soil samples were obtained from Jiaozhou Bay in January, April, July, and October of 2014. Results showed that the DOM contents in soil of four typical wetland were in order of spartina wetland > naked tidal > suaeda salsa wetland > reed wetland in horizontal direction, and decreased with the increase of soil depth on vertical section. In addition, the DOM contents changed with the seasons, in order of spring > summer > autumn > winter. The structural characteristics of DOM in Jiaozhou Bay wetland, such as aromaticity, hydrophobicity, molecular weight, polymerization degree of benzene ring carbon frame structure and so on were in order of spartina wetland > naked tidal > suaeda salsa wetland > reed wetland in the horizontal direction. On the vertical direction, they showed a decreasing trend with the increase of soil depth. The results of three dimensional fluorescence spectra and fluorescence spectrum parameters (FI, HIX, and BIX) indicated that the DOM in Jiaozhou Bay was mainly derived from the biological activities. The contents and structure of DOM had certain relevance, but the contents and source as well as the structure and source of DOM had no significant correlation. The external pollution including domestic sewage, industrial wastewater, and aquaculture sewage affected the correlation among the content, structure and source of DOM by influencing the percentage of non-fluorescent substance in DOM and disturbing the determination of protein-like fluorescence.

Contrasting elevational diversity patterns for soil bacteria between two ecosystems divided by the treeline.

PubMed

Li, Guixiang; Xu, Guorui; Shen, Congcong; Tang, Yong; Zhang, Yuxin; Ma, Keming

2016-11-01

Above- and below-ground organisms are closely linked, but how elevational distribution pattern of soil microbes shifting across the treeline still remains unknown. Sampling of 140 plots with transect, we herein investigated soil bacterial distribution pattern from a temperate forest up to a subalpine meadow along an elevational gradient using Illumina sequencing. Our results revealed distinct elevational patterns of bacterial diversity above and below the treeline in responding to changes in soil conditions: a hollow elevational pattern in the forest (correlated with soil temperature, pH, and C:N ratio) and a significantly decreasing pattern in the meadow (correlated with soil pH, and available phosphorus). The bacterial community structure was also distinct between the forest and meadow, relating to soil pH in the forest and soil temperature in the meadow. Soil bacteria did not follow the distribution pattern of herb diversity, but bacterial community structure could be predicted by herb community composition. These results suggest that plant communities have an important influence on soil characteristics, and thus change the elevational distribution of soil bacteria. Our findings are useful for future assessments of climate change impacts on microbial community.

Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter.

PubMed

Sun, Ruibo; Dsouza, Melissa; Gilbert, Jack A; Guo, Xisheng; Wang, Daozhong; Guo, Zhibin; Ni, Yingying; Chu, Haiyan

2016-12-01

Organic matter application is a widely used practice to increase soil carbon content and maintain soil fertility. However, little is known about the effect of different types of organic matter, or the input of exogenous species from these materials, on soil fungal communities. In this study, fungal community composition was characterized from soils amended with three types of organic matter over a 30-year fertilization experiment. Chemical fertilization significantly changed soil fungal community composition and structure, which was exacerbated by the addition of organic matter, with the direction of change influenced by the type of organic matter used. The addition of organic matter significantly increased soil fungal richness, with the greatest richness achieved in soils amended with pig manure. Importantly, following addition of cow and pig manure, fungal taxa associated with these materials could be found in the soil, suggesting that these exogenous species can augment soil fungal composition. Moreover, the addition of organic matter decreased the relative abundance of potential pathogenic fungi. Overall, these results indicate that organic matter addition influences the composition and structure of soil fungal communities in predictable ways. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Rheological properties of soil: a review

NASA Astrophysics Data System (ADS)

Zhu, Guangli; Zhu, Long; Yu, Chao

2017-05-01

Recently rheological methods have been applied to investigate the mechanical properties of soil micro-structure. Rheological techniques have a number of quantitative physically based measurements and offer a better understanding of how soil micro-structure behaves when subject to stress. Rheological material is refers to deformation properties similar to the solid and flow properties similar to the liquid of bound water and colloidal substances under stress. Soil rheology is divided into fluid rheology and plasticity rheology. Fluid rheology is produced by rheological material. Plasticity rheology mainly refers to the sliding and peristaltic between soil solid particles under shear stress. It is generally believed that the soft soil rheology mainly belongs to fluid rheology, while the rheology of sand and other coarse grained soil mainly belongs to plasticity rheology. Thus, rheology mechanisms of soft soil and sand are different. This paper introduces the methods of the research progress on the rheology of soil, in the soil rheological mechanism, rheological model and rheological numerical aspects of the research at home and abroad were summarized and analysed, discussed the problems existed in related research, and puts forward some suggestions for the future study on the rheology of soil.

Factors Affecting Performance of Soil Termiticides

USDA-ARS?s Scientific Manuscript database

Applying liquid insecticide to soil under and around structures is one of the most widely used methods of subterranean termite prevention and control. Failure of soil termiticide treatments is often related to factors other than the active ingredient. Efficacy and longevity of soil treatments vary g...

The Vertical Structure of Urban Soils - Portland

EPA Science Inventory

We compared observed to reference pedons for two cities (Detroit MI; Cleveland OH), where it was clearly illustrated that urban soils had fewer soil horizons than their non-urban references. The ordering of observed urban soil horizons was distinct from both the theoretical (A-B-...

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

PubMed Central

Lima-Morales, Daiana; Jáuregui, Ruy; Camarinha-Silva, Amelia; Geffers, Robert; Vilchez-Vargas, Ramiro

2016-01-01

Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched. PMID:26850298

Effect of soil properties, heavy metals and emerging contaminants in the soil nematodes diversity.

PubMed

Gutiérrez, Carmen; Fernández, Carlos; Escuer, Miguel; Campos-Herrera, Raquel; Beltrán Rodríguez, Mª Eulalia; Carbonell, Gregoria; Rodríguez Martín, Jose Antonio

2016-06-01

Among soil organisms, nematodes are seen as the most promising candidates for bioindications of soil health. We hypothesized that the soil nematode community structure would differ in three land use areas (agricultural, forest and industrial soils), be modulated by soil parameters (N, P, K, pH, SOM, CaCO3, granulometric fraction, etc.), and strongly affected by high levels of heavy metals (Cd, Pb, Zn, Cr, Ni, Cu, and Hg) and emerging contaminants (pharmaceuticals and personal care products, PPCPs). Although these pollutants did not significantly affect the total number of free-living nematodes, diversity and structure community indices vastly altered. Our data showed that whereas nematodes with r-strategy were tolerant, genera with k-strategy were negatively affected by the selected pollutants. These effects diminished in soils with high levels of heavy metals given their adaptation to the historical pollution in this area, but not to emerging pollutants like PPCPs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of the inoculant strain Sphingomonas paucimobilis 20006FA on soil bacterial community and biodegradation in phenanthrene-contaminated soil.

PubMed

Coppotelli, B M; Ibarrolaza, A; Del Panno, M T; Morelli, I S

2008-02-01

The effects of the inoculant strain Sphingomonas paucimobilis 20006FA (isolated from a phenanthrene-contaminated soil) on the dynamics and structure of microbial communities and phenanthrene elimination rate were studied in soil microcosms artificially contaminated with phenanthrene. The inoculant managed to be established from the first inoculation as it was evidenced by denaturing gradient gel electrophoresis analysis, increasing the number of cultivable heterotrophic and PAH-degrading cells and enhancing phenanthrene degradation. These effects were observed only during the inoculation period. Nevertheless, the soil biological activity (dehydrogenase activity and CO(2) production) showed a late increase. Whereas gradual and successive changes in bacterial community structures were caused by phenanthrene contamination, the inoculation provoked immediate, significant, and stable changes on soil bacterial community. In spite of the long-term establishment of the inoculated strain, at the end of the experiment, the bioaugmentation did not produce significant changes in the residual soil phenanthrene concentration and did not improve the residual effects on the microbial soil community.

Profile analysis of microbiomes in soils of solonetz complex in the Caspian Lowland

NASA Astrophysics Data System (ADS)

Chernov, T. I.; Lebedeva, M. P.; Tkhakakhova, A. K.; Kutovaya, O. V.

2017-01-01

The taxonomic structure of the microbiota in two associated soils—solonetz on a microhigh and meadow-chestnut soil in a microlow—was studied in the semidesert of the Caspian Lowland. A highthroughput sequencing of the 16S rRNA gene was used for the soil samples from genetic horizons. A considerable reduction in the bacterial diversity was found in the lower horizons of the solonetz and compact solonetzic horizon with a high content of exchangeable sodium. In the meadow-chestnut soil, the microbial diversity little decreased with the depth. In both soils, a portion of archaea from the Thaumarchaeota group also decreased in the deeper horizons. In the soil horizons with the lower total bacterial diversity, a share of proteobacteria of the Enterobacteriaceae, Pseudomonadaceae, and Sphingomonadaceae families became higher. The difference between the structure of the microbial population in the solonetz and meadow- chestnut soil can be first explained by the different water regimes and soil consistence.

Soil structural stability assessment with the fluidized bed, aggregate stability, and rainfall simulation on long-term tillage and crop rotation systems

USDA-ARS?s Scientific Manuscript database

The formation of stable soil aggregates is an important indicator of soil susceptibility to erosion and a factor defining soil health. On cropland, tillage practices and crop rotations have shown to control soil biophysical properties with potential consequences on erosion susceptibility. Thus, the ...

Seismic response of elevated rectangular water tanks considering soil structure interaction

NASA Astrophysics Data System (ADS)

Visuvasam, J.; Simon, J.; Packiaraj, J. S.; Agarwal, R.; Goyal, L.; Dhingra, V.

2017-11-01

The overhead staged water tanks are susceptible for high lateral forces during earthquakes. Due to which, the failure of beam-columns joints, framing elements and toppling of tanks arise. To avoid such failures, they are analyzed and designed for lateral forced induced by devastating earthquakes assuming the base of the structures are fixed and considering functional needs, response reduction, soil types and severity of ground shaking. In this paper, the flexible base was provided as spring stiffness in order to consider the effect of soil properties on the seismic behaviour of water tanks. A linear time history earthquake analysis was performed using SAP2000. Parametric studies have been carried out based on various types of soils such as soft, medium and hard. The soil stiffness values highly influence the time period and base shear of the structure. The ratios of time period of flexible to fixed base and base shear of flexible to fixed base were observed against capacities of water tank and the overall height of the system. The both responses are found to be increased as the flexibility of soil medium decreases

75 FR 55479 - National Oil and Hazardous Substances Pollution Contingency Plan; National Priorities List...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-13

... surface media (soil, surface water, sediment) and structures (both former structures that have been... . SUPPLEMENTARY INFORMATION: The portion of the site to be deleted from the NPL is the surface media (soil...

Sorption of Hydrophobic Organic Compounds on Natural Sorbents and Organoclays from Aqueous and Non-Aqueous Solutions: A Mini-Review

PubMed Central

Moyo, Francis; Tandlich, Roman; Wilhelmi, Brendan S.; Balaz, Stefan

2014-01-01

Renewed focus on the sorption of hydrophobic organic chemicals (HOCs) onto mineral surfaces and soil components is required due to the increased and wider range of organic pollutants being released into the environment. This mini-review examines the possibility of the contribution and mechanism of HOC sorption onto clay mineral sorbents such as kaolinite, and soil organic matter and the possible role of both in the prevention of environmental contamination by HOCs. Literature data indicates that certain siloxane surfaces can be hydrophobic. Therefore soils can retain HOCs even at low soil organic levels and the extent will depend on the structure of the pollutant and the type and concentration of clay minerals in the sorbent. Clay minerals are wettable by nonpolar solvents and so sorption of HOCs onto them from aqueous and non-aqueous solutions is possible. This is important for two reasons: firstly, the movement and remediation of soil environments will be a function of the concentration and type of clay minerals in the soil. Secondly, low-cost sorbents such as kaolinite and expandable clays can be added to soils or contaminated environments as temporary retention barriers for HOCs. Inorganic cations sorbed onto the kaolinite have a strong influence on the rate and extent of sorption of hydrophobic organic pollutants onto kaolinite. Structural sorbate classes that can be retained by the kaolinite matrix are limited by hydrogen bonding between hydroxyl groups of the octahedral alumosilicate sheet and the tetrahedral sheet with silicon. Soil organic carbon plays a key role in the sorption of HOCs onto soils, but the extent will be strongly affected by the structure of the organic soil matter and the presence of soot. Structural characterisation of soil organic matter in a particular soil should be conducted during a particular contamination event. Contamination by mining extractants and antibiotics will require renewed focus on the use of the QSAR approaches in the context of the sorption of HOCs onto clay minerals from aqueous and non-aqueous solutions. PMID:24821385

Response analysis of a nuclear containment structure with nonlinear soil-structure interaction under bi-directional ground motion

NASA Astrophysics Data System (ADS)

Kumar, Santosh; Raychowdhury, Prishati; Gundlapalli, Prabhakar

2015-06-01

Design of critical facilities such as nuclear power plant requires an accurate and precise evaluation of seismic demands, as any failure of these facilities poses immense threat to the community. Design complexity of these structures reinforces the necessity of a robust 3D modeling and analysis of the structure and the soil-foundation interface. Moreover, it is important to consider the multiple components of ground motion during time history analysis for a realistic simulation. Present study is focused on investigating the seismic response of a nuclear containment structure considering nonlinear Winkler-based approach to model the soil-foundation interface using a distributed array of inelastic springs, dashpots and gap elements. It is observed from this study that the natural period of the structure increases about 10 %, whereas the force demands decreases up to 24 % by considering the soil-structure interaction. Further, it is observed that foundation deformations, such as rotation and sliding are affected by the embedment ratio, indicating an increase of up to 56 % in these responses for a reduction of embedment from 0.5 to 0.05× the width of the footing.

Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India

PubMed Central

2012-01-01

Background Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO2 dynamics in soil. In this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). We studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbL encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The cbbL form IA and IC genes associated with carbon fixation were analyzed to gain insight into metabolic potential of chemolithoautotrophs in three soil types of coastal ecosystems which had a very different salt load and sulphur content. Results In cbbL libraries, the cbbL form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC cbbL was also amplified from bacterial isolates obtained from all soil types. A number of novel monophyletic lineages affiliated with form IA and IC phylogenetic trees were found. These were distantly related to the known cbbL sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (Betaproteobacteria) whereas photoautotrophic Chloroflexi and sulphide oxidizers dominated saline ecosystems. Environmental specificity was apparently visible at both higher taxonomic levels (phylum) and lower taxonomic levels (genus and species). The differentiation in community structure and diversity in three soil ecosystems was supported by LIBSHUFF (P = 0.001) and UniFrac. Conclusion This study may provide fundamentally new insights into the role of chemolithoautotrophic and photoautotrophic bacterial diversity in biochemical carbon cycling in barren saline soils. The bacterial communities varied greatly among the three sites, probably because of differences in salinity, carbon and sulphur contents. The cbbL form IA-containing sulphide-oxidizing chemolithotrophs were found only in high saline soil clone library, thus giving the indication of sulphide availability in this soil ecosystem. This is the first comparative study of the community structure and diversity of chemolithoautotrophic bacteria in coastal agricultural and saline barren soils using functional (cbbL) and phylogenetic (16S rDNA) marker genes. PMID:22834535

Soil bacterial community responses to revegetation of moving sand dune in semi-arid grassland.

PubMed

Cao, Chengyou; Zhang, Ying; Cui, Zhenbo; Feng, Shuwei; Wang, Tingting; Ren, Qing

2017-08-01

Grasslands in semi-arid Northern China are widely desertified, thus inducing the formation of a large area of moving sand lands. Revegetation of the sandy land is commonly adopted to restore degraded grasslands. The structure of the soil microbial community might dramatically change during degradation and recovery because microorganisms are one of the major drivers of ecological process through their interactions with plants and soil. Assuming that soil properties are the key determinants of the structure of soil bacterial community within the same soil type, whether the vegetation type causes the significant difference in the structure of soil bacterial community during revegetation and restoration of the degraded grasslands remains poorly understood. Our study aimed to (1) investigate the response of soil bacterial communities to the changes during vegetation degradation and recovery and (2) evaluate whether the soil bacterial communities under plantations return to their native state. We detected the shifts in diversities and compositions of the soil bacterial communities and the relative abundance of dominant bacterial taxa by using the high-throughput Illumina MiSeq sequencing technique in an area covered by 32-year-old Caragana microphylla, Artemisia halodendron, Hedysarum fruticosum, Pinus sylvestris var. mongolica, Populus simonii, and Salix gordejevii sand-fixing plantations and in the native community (NC) dominated by elm, and moving sandy dune (MS). We found that the obtained operational taxonomic units by 16S rRNA gene sequencing and diversity index in MS were all significantly lower than those in NC, and the number and composition of dominant genera were significantly different between NC and MS. Interestingly, the compositions of bacterial communities and the dominant genera in different sand-fixation plantations (C. microphylla, A. halodendron, H. fruticosum, P. sylvestris var. mongolica, P. simonii, and S. gordejevii) were all similar to those of the native soil of NC, suggesting that the plantation type and soil properties exhibit a minimal effect on the compositions of soil microbial communities within a continuous landscape. These results revealed that the structure of the soil bacterial community of degraded sandy grassland (even degenerated into a mobile sand dunes) in semi-arid region can be reversibly restored by planting indigenous shrub or semi-shrub plantation on human time scales.

Copper pollution decreases the resistance of soil microbial community to subsequent dry-rewetting disturbance.

PubMed

Li, Jing; Wang, Jun-Tao; Hu, Hang-Wei; Ma, Yi-Bing; Zhang, Li-Mei; He, Ji-Zheng

2016-01-01

Dry-rewetting (DW) disturbance frequently occurs in soils due to rainfall and irrigation, and the frequency of DW cycles might exert significant influences on soil microbial communities and their mediated functions. However, how microorganisms respond to DW alternations in soils with a history of heavy metal pollution remains largely unknown. Here, soil laboratory microcosms were constructed to explore the impacts of ten DW cycles on the soil microbial communities in two contrasting soils (fluvo-aquic soil and red soil) under three copper concentrations (zero, medium and high). Results showed that the fluctuations of substrate induced respiration (SIR) decreased with repeated cycles of DW alternation. Furthermore, the resistance values of substrate induced respiration (RS-SIR) were highest in non-copper-stressed (zero) soils. Structural equation model (SEM) analysis ascertained that the shifts of bacterial communities determined the changes of RS-SIR in both soils. The rate of bacterial community variance was significantly lower in non-copper-stressed soil compared to the other two copper-stressed (medium and high) soils, which might lead to the higher RS-SIR in the fluvo-aquic soil. As for the red soil, the substantial increase of the dominant group WPS-2 after DW disturbance might result in the low RS-SIR in the high copper-stressed soil. Moreover, in both soils, the bacterial diversity was highest in non-copper-stressed soils. Our results revealed that initial copper stress could decrease the resistance of soil microbial community structure and function to subsequent DW disturbance. Copyright © 2015. Published by Elsevier B.V.

Environmental and management influences on temporal variability of near saturated soil hydraulic properties.

PubMed

Bodner, G; Scholl, P; Loiskandl, W; Kaul, H-P

2013-08-01

Structural porosity is a decisive property for soil productivity and soil environmental functions. Hydraulic properties in the structural range vary over time in response to management and environmental influences. Although this is widely recognized, there are few field studies that determine dominant driving forces underlying hydraulic property dynamics. During a three year field experiment we measured temporal variability of soil hydraulic properties by tension infiltrometry. Soil properties were characterized by hydraulic conductivity, effective macroporosity and Kosugi's lognormal pore size distribution model. Management related influences comprised three soil cover treatment (mustard and rye vs. fallow) and an initial mechanical soil disturbance with a rotary harrow. Environmental driving forces were derived from meteorological and soil moisture data. Soil hydraulic parameters varied over time by around one order of magnitude. The coefficient of variation of soil hydraulic conductivity K(h) decreased from 69.5% at saturation to 42.1% in the more unsaturated range (- 10 cm pressure head). A slight increase in the Kosugi parameter showing pore heterogeneity was observed under the rye cover crop, reflecting an enhanced structural porosity. The other hydraulic parameters were not significantly influenced by the soil cover treatments. Seedbed preparation with a rotary harrow resulted in a fourfold increase in macroporosity and hydraulic conductivity next to saturation, and homogenized the pore radius distribution. Re-consolidation after mechanical loosening lasted over 18 months until the soil returned to its initial state. The post-tillage trend of soil settlement could be approximated by an exponential decay function. Among environmental factors, wetting-drying cycles were identified as dominant driving force explaining short term hydraulic property changes within the season (r 2  = 0.43 to 0.59). Our results suggested that beside considering average management induced changes in soil properties (e.g. cover crop introduction), a dynamic approach to hydrological modeling is required to capture over-seasonal (tillage driven) and short term (environmental driven) variability in hydraulic parameters.

The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

NASA Astrophysics Data System (ADS)

Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

2011-12-01

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial communities, while the quality of available organic matter may have played a significant role in supporting high performing microbial communities.

Environmental and management influences on temporal variability of near saturated soil hydraulic properties☆

PubMed Central

Bodner, G.; Scholl, P.; Loiskandl, W.; Kaul, H.-P.

2013-01-01

Structural porosity is a decisive property for soil productivity and soil environmental functions. Hydraulic properties in the structural range vary over time in response to management and environmental influences. Although this is widely recognized, there are few field studies that determine dominant driving forces underlying hydraulic property dynamics. During a three year field experiment we measured temporal variability of soil hydraulic properties by tension infiltrometry. Soil properties were characterized by hydraulic conductivity, effective macroporosity and Kosugi's lognormal pore size distribution model. Management related influences comprised three soil cover treatment (mustard and rye vs. fallow) and an initial mechanical soil disturbance with a rotary harrow. Environmental driving forces were derived from meteorological and soil moisture data. Soil hydraulic parameters varied over time by around one order of magnitude. The coefficient of variation of soil hydraulic conductivity K(h) decreased from 69.5% at saturation to 42.1% in the more unsaturated range (− 10 cm pressure head). A slight increase in the Kosugi parameter showing pore heterogeneity was observed under the rye cover crop, reflecting an enhanced structural porosity. The other hydraulic parameters were not significantly influenced by the soil cover treatments. Seedbed preparation with a rotary harrow resulted in a fourfold increase in macroporosity and hydraulic conductivity next to saturation, and homogenized the pore radius distribution. Re-consolidation after mechanical loosening lasted over 18 months until the soil returned to its initial state. The post-tillage trend of soil settlement could be approximated by an exponential decay function. Among environmental factors, wetting-drying cycles were identified as dominant driving force explaining short term hydraulic property changes within the season (r2 = 0.43 to 0.59). Our results suggested that beside considering average management induced changes in soil properties (e.g. cover crop introduction), a dynamic approach to hydrological modeling is required to capture over-seasonal (tillage driven) and short term (environmental driven) variability in hydraulic parameters. PMID:24748683

Predicting effects of climate change on the composition and function of soil microbial communities

NASA Astrophysics Data System (ADS)

Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

2008-12-01

Complex soil microbial communities regulate critical ecosystem processes that will be altered by climate change. A critical step towards predicting the impacts of climate change on terrestrial ecosystems is to determine the primary controllers of soil microbial community composition and function, and subsequently evaluate climate change scenarios that alter these controllers. We surveyed complex soil bacterial and archaeal communities across a range of climatic and edaphic conditions to identify critical controllers of soil microbial community composition in the field and then tested the resulting predictions using a 2-year manipulation of precipitation and temperature using mesocosms of California annual grasslands. Community DNA extracted from field soils sampled from six different ecosystems was assayed for bacterial and archaeal communities using high-density phylogenetic microarrays as well as functional gene arrays. Correlations among the relative abundances of thousands of microbial taxa and edaphic factors such as soil moisture and nutrient content provided a basis for predicting community responses to changing soil conditions. Communities of soil bacteria and archaea were strongly structured by single environmental predictors, particularly variables related to soil water. Bacteria in the Actinomycetales and Bacilli consistently demonstrated a strong negative response to increasing soil moisture, while taxa in a greater variety of lineages responded positively to increasing soil moisture. In the climate change experiment, overall bacterial community structure was impacted significantly by total precipitation but not by plant species. Changes in soil moisture due to decreased rainfall resulted in significant and predictable alterations in community structure. Over 70% of the bacterial taxa in common with the cross-ecosystem study responded as predicted to altered precipitation, with the most conserved response from Actinobacteria. The functional consequences of these predictable changes in community composition were measured with functional arrays that detect genes involved in the metabolism of carbon, nitrogen and other elements. The response of soil microbial communities to altered precipitation can be predicted from the distribution of microbial taxa across moisture gradients.

Impact of land management on soil structure and soil hydraulic properties

NASA Astrophysics Data System (ADS)

Kodesova, Radka; Jirku, Veronika; Nikodem, Antonin; Muhlhanselova, Marcela; Zigova, Anna

2010-05-01

Study is focused on a comparison of a soil structure and soil hydraulic properties within soil profiles of a same soil type under different land management. Study was performed in Haplic Luvisol in Hnevceves the Czech Republic. Two soil profiles, which were in close distance from each other, were chosen: 1. under the conventional tillage, 2. under the permanent (30 years) grass cover. Soil sampling and field experiments were carried out immediately after the harvest of winter barley in 2008. The micromorphological images were used to evaluate the soil structure of all Ap, Bt1, Bt2 and C diagnostic horizons. The hydraulic properties of the diagnostic horizons were studied in the laboratory using multistep outflow experiments performed on the undisturbed 100-cm3 soil samples. A tension disc infiltrometer (with a disc radius of 10 cm) and minidisc tension infiltrometers (with a disc radius of 2.2 cm) were used to measure cumulative water infiltration under unsaturated conditions created using a pressure head of -2 cm. Measurements were performed at a depths of 5, 45, 75 and 110 cm, which corresponded to the Ap, Bt1, Bt2 and C horizons of studied Haplic Luvisol at both locations. The Guelph permeameter was used to measure cumulative water flux under surface ponding conditions. The depth of the drilled well was 10, 50, 80 and 115 cm, the well radius was 3 cm, and the well ponding depth was 5 cm. Both tests were used to evaluate hydraulic conductivity (K for h=-2cm, and Ks) values. Results showed, that while properties in the Bt2 and C horizons of both soil profiles were relatively similar, properties in the Ap and Bt1 horizons were different. The fraction of gravitational pores (which may cause preferential flow) in the Ap and Bt1 horizons of the soil profile under the convectional tillage was large than those in the Ap and Bt1 horizons of the soil profile under the permanent grass. This influenced for instance the Ks values measured using the Guelph permeametr. The Ks values were higher and more variable in the soil profile under the convectional tillage than those in the soil profile under the permanent grass. On the other hand, due to the periodical tillage and consequent soil structure breakdown, the fraction of the large capillary pores were smaller in the Ap horizon of the soil profile under the convectional tillage than that in the Ap horizon of the soil profile under the permanent grass. As result the K (h=-2cm) values measured using the tension infiltrometer in the soil profile under the permanent grass was higher than those in the soil profile under the convectional tillage. However, the fraction of the large capillary pores and K (h=-2cm) values were similar in the Bt1 horizons of both soil profiles. Thus the land management impacted both macropores and matrix pores in the Ap horizon and macropores (prismatic structure and biopores) in the Bt1 horizon. Acknowledgement: Authors acknowledge the financial support of the Grant Agency of the Czech Republic (grant No. GA CR 526/08/0434) and the Ministry of Education, Youth and Sports of the Czech Republic (grant No. MSM 6046070901).

Preliminary Guidelines and Standard Operating Procedure for Drainage and Erosion Control at McMurdo Station

DTIC Science & Technology

2014-12-01

along the impermeable frozen soil layer. Soil freeze–thaw action disrupts soil structures, displaces soils particles , and creates voids both in...discharging along the bank face). This was caused by excess pore water pressure. Soil piping removes soil particles from their in-situ position, leaving...soil particles ERDC/CRREL SR-14-3 30 c. Maintain original side and bed slopes during the clearing efforts. d. Shape the channels to minimize

Spatial characterization of soil properties and influence in soil formation in oak-grassland of Sierra Morena, S Spain

NASA Astrophysics Data System (ADS)

Román-Sánchez, Andrea; Cáceres, Francisco; Pédèches, Remi; Giráldez Cervera, Juan Vicente; Vanwalleghem, Tom

2016-04-01

The Mediterranean oak-grassland ecosystem is very important for the rural economy and for the biodiversity of south-western European countries like Spain and Portugal. Nevertheless these ecosystems are not well characterized especially their soils. In this report soil carbon has been evaluated and related to other properties. The principal factors controlling the structure, productivity and evolution of forest ecosystems are bedrock, climate, relief, vegetation and time. Soil carbon has an important influence in the soil and ecosystem structures. The purpose of this study is to determine the relationship between relief, soil properties, spatial distribution of soil carbon and their influence in soil formation and geomorphology. This work is part of another study which aims to elucidate the processes involved in the soil formation and to examine their behaviour on long-term with a modelling. In our study area, located in oak-grassland of Sierra Morena, in Cordoba, S Spain, have been studied 67 points at 6 depths in 262 hectares in order to determine carbon content varying between 0-6%, soil properties such as soil depth between 0-4 m, horizon depth and the rocks amount in surface. The relationship between the soil carbon, soil properties and the relief characteristic like slope, aspect, curvature can shed light the processes that affect the mechanisms of bedrock weathering and their interrelationship with geomorphological processes.

Biogeochemical drivers of microbial community convergence across actively retreating glaciers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castle, Sarah C.; Nemergut, Diana R.; Grandy, A. Stuart

The ecological processes that influence biogeographical patterns of microorganisms are actively debated. To investigate how such patterns emerge during ecosystem succession, we examined the biogeochemical drivers of bacterial community assembly in soils over two environmentally distinct, recently deglaciated chronosequences separated by a distance of more than 1,300 kilometers. Our results show that despite different geographic, climatic, and soil chemical and physical characteristics at the two sites, soil bacterial community structure and decomposer function converged during plant succession. In a comparative analysis, we found that microbial communities in early succession soils were compositionally distinct from a group of diverse, mature forestmore » soils, but that the differences between successional soils and mature soils decreased from early to late stages of succession. Differences in bacterial community composition across glacial sites were largely explained by pH. However, successional patterns and community convergence across sites were more consistently related to soil organic carbon and organic matter chemistry, which appeared to be tightly coupled with bacterial community structure across both young and mature soils.« less

Uncertainty in Ecohydrological Modeling in an Arid Region Determined with Bayesian Methods

PubMed Central

Yang, Junjun; He, Zhibin; Du, Jun; Chen, Longfei; Zhu, Xi

2016-01-01

In arid regions, water resources are a key forcing factor in ecosystem circulation, and soil moisture is the critical link that constrains plant and animal life on the soil surface and underground. Simulation of soil moisture in arid ecosystems is inherently difficult due to high variability. We assessed the applicability of the process-oriented CoupModel for forecasting of soil water relations in arid regions. We used vertical soil moisture profiling for model calibration. We determined that model-structural uncertainty constituted the largest error; the model did not capture the extremes of low soil moisture in the desert-oasis ecotone (DOE), particularly below 40 cm soil depth. Our results showed that total uncertainty in soil moisture prediction was improved when input and output data, parameter value array, and structure errors were characterized explicitly. Bayesian analysis was applied with prior information to reduce uncertainty. The need to provide independent descriptions of uncertainty analysis (UA) in the input and output data was demonstrated. Application of soil moisture simulation in arid regions will be useful for dune-stabilization and revegetation efforts in the DOE. PMID:26963523

Effects of the soil pore network architecture on the soil's physical functionalities

NASA Astrophysics Data System (ADS)

Smet, Sarah; Beckers, Eléonore; Léonard, Angélique; Degré, Aurore

2017-04-01

The soil fluid movement's prediction is of major interest within an agricultural or environmental scope because many processes depend ultimately on the soil fluids dynamic. It is common knowledge that the soil microscopic pore network structure governs the inner-soil convective fluids flow. There isn't, however, a general methodthat consider the pore network structure as a variable in the prediction of thecore scale soil's physical functionalities. There are various possible representations of the microscopic pore network: sample scale averaged structural parameters, extrapolation of theoretic pore network, or use of all the information available by modeling within the observed pore network. Different representations implydifferent analyzing methodologies. To our knowledge, few studies have compared the micro-and macroscopic soil's characteristics for the same soil core sample. The objective of our study is to explore the relationship between macroscopic physical properties and microscopic pore network structure. The saturated hydraulic conductivity, the air permeability, the retention curve, and others classical physical parameters were measured for ten soil samples from an agricultural field. The pore network characteristics were quantified through the analyses of X-ray micro-computed tomographic images(micro-CT system Skyscan-1172) with a voxel size of 22 µm3. Some of the first results confirmed what others studies had reported. Then, the comparison between macroscopic properties and microscopic parameters suggested that the air movements depended mostly on the pore connectivity and tortuosity than on the total porosity volume. We have also found that the fractal dimension calculated from the X-ray images and the fractal dimension calculated from the retention curve were significantly different. Our communication will detailthose results and discuss the methodology: would the results be similar with a different voxel size? What are the calculated and measured parameters uncertainties? Sarah Smet, as a research fellow, acknowledges the support of the National Fund for Scientific Research (Brussels, Belgium).

The impact of biofumigation and chemical fumigation methods on the structure and function of the soil microbial community.

PubMed

Omirou, Michalis; Rousidou, Constantina; Bekris, Fotios; Papadopoulou, Kalliope K; Menkissoglou-Spiroudi, Urania; Ehaliotis, Constantinos; Karpouzas, Dimitrios G

2011-01-01

Biofumigation (BIOF) is carried out mainly by the incorporation of brassica plant parts into the soil, and this fumigation activity has been linked to their high glucosinolate (GSL) content. GSLs are hydrolyzed by the endogenous enzyme myrosinase to release isothiocyanates (ITCs). A microcosm study was conducted to investigate the effects induced on the soil microbial community by the incorporation of broccoli residues into soil either with (BM) or without (B) added myrosinase and of chemical fumigation, either as soil application of 2-phenylethyl ITC (PITC) or metham sodium (MS). Soil microbial activity was evaluated by measuring fluorescein diacetate hydrolysis and soil respiration. Effects on the structure of the total microbial community were assessed by phospholipid fatty acid analysis, while the impact on important fungal (ascomycetes (ASC)) and bacterial (ammonia-oxidizing bacteria (AOB)) guilds was evaluated by denaturating gradient gel electrophoresis (DGGE). Overall, B, and to a lesser extent BM, stimulated microbial activity and biomass. The diminished effect of BM compared to B was particularly evident in fungi and Gram-negative bacteria and was attributed to rapid ITC release following the myrosinase treatment. PITC did not have a significant effect, whereas an inhibitory effect was observed in the MS-treated soil. DGGE analysis showed that the ASC community was temporarily altered by BIOF treatments and more persistently by the MS treatment, while the structure of the AOB community was not affected by the treatments. Cloning of the ASC community showed that MS application had a deleterious effect on potential plant pathogens like Fusarium, Nectria, and Cladosporium compared to BIOF treatments which did not appear to inhibit them. Our findings indicate that BIOF induces changes on the structure and function of the soil microbial community that are mostly related to microbial substrate availability changes derived from the soil amendment with fresh organic materials.

Crossing Phenomena in Overhead Line Equipment (OHLE) Structure in 3D Space Considering Soil-Structure Interaction

NASA Astrophysics Data System (ADS)

Ngamkhanong, Chayut; Kaewunruen, Sakdirat; Baniotopoulos, Charalampos; Papaelias, Mayorkinos

2017-10-01

Nowadays, the electric train becomes one of the efficient railway systems that are lighter, cleaner, quieter, cheaper and faster than a conventional train. Overhead line equipment (OHLE), which supplies electric power to the trains, is designed on the principle of overhead wires placed over the railway track. The OHLE is supported by mast structure which located at the lineside along the track. Normally, mast structure is a steel column or truss structure which supports the overhead wire carrying the power. Due to the running train and severe periodic force, such as an earthquake, in surrounding area may cause damage to the OHLE structure especially mast structure which leads to the failure of the electrical system. The mast structure needs to be discussed in order to resist the random forces. Due to the vibration effect, the natural frequencies of the structure are necessary. This is because when the external applied force occurs within a range of frequency of the structure, resonance effect can be expected which lead to the large oscillations and deflections. The natural frequency of a system is dependent only on the stiffness of the structure and the mass which participates with the structure, including self-weight. The modal analysis is used in order to calculate the mode shapes and natural frequencies of the mast structure during free vibration. A mast structure with varying rotational soil stiffness is used to observe the influence of soil-structure action. It is common to use finite element analysis to perform a modal analysis. This paper presents the fundamental mode shapes, natural frequencies and crossing phenomena of three-dimensional mast structure considering soil-structure interaction. The sensitivity of mode shapes to the variation of soil-structure interaction is discussed. The outcome of this study will improve the understanding of the fundamental dynamic behaviour of the mast structure which supports the OHLE. Moreover, this study will be a recommendation for the structural engineer to associate with the behaviour of mast structure during vibration.

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

PubMed

Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

2017-05-01

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Soil microbial community structure: mechanical disturbance alters soil microbial community

USDA-ARS?s Scientific Manuscript database

Soil microbes are responsible for soil nutrient cycling in both perennial and annual management systems for beef cattle and grain production. In the Southern Plains of Oklahoma, producers plant winter wheat (Triticum aestivum) in rotation with winter canola (Brassica rapa). Producers in the Southern...

Soil fungal communities respond to grassland plant community richness and soil edaphics

USDA-ARS?s Scientific Manuscript database

Fungal communities in soil have significant influences on terrestrial ecosystem dynamics, yet our understanding of the drivers of fungal diversity and community structure in soil is limited. Fungal communities associated with the rhizosphere of four native perennial grassland plant species grown in ...

Anaerobic soil disinfestation and Brassica seed meal amendment alter soil microbiology and system resistance

USDA-ARS?s Scientific Manuscript database

Brassica seed meal amendments and anaerobic soil disinfestation control a spectrum of soil-borne plant pathogens via a diversity of mechanisms. Transformations in microbial community structure and function in certain instances were determinants of disease control and enhanced plant performance. Fo...

NEGLECTED COMPONENTS OF BIODIVERSITY: SOIL ORIBATID MITES, COMMUNITY STRUCTURE AND SOIL RECOVERY

EPA Science Inventory

Oribatid mites are an abundant and diverse component of soils in regional pine forests, and are valuable in characterizing the biodiversity of these forested lands. We sampled oribatid mites using soil cores and leaf litterbags, in young aggrading forest stands. Comparing these...

Regional-Scale Drivers of Forest Structure and Function in Northwestern Amazonia

PubMed Central

Higgins, Mark A.; Asner, Gregory P.; Anderson, Christopher B.; Martin, Roberta E.; Knapp, David E.; Tupayachi, Raul; Perez, Eneas; Elespuru, Nydia; Alonso, Alfonso

2015-01-01

Field studies in Amazonia have found a relationship at continental scales between soil fertility and broad trends in forest structure and function. Little is known at regional scales, however, about how discrete patterns in forest structure or functional attributes map onto underlying edaphic or geological patterns. We collected airborne LiDAR (Light Detection and Ranging) data and VSWIR (Visible to Shortwave Infrared) imaging spectroscopy measurements over 600 km2 of northwestern Amazonian lowland forests. We also established 83 inventories of plant species composition and soil properties, distributed between two widespread geological formations. Using these data, we mapped forest structure and canopy reflectance, and compared them to patterns in plant species composition, soils, and underlying geology. We found that variations in soils and species composition explained up to 70% of variation in canopy height, and corresponded to profound changes in forest vertical profiles. We further found that soils and plant species composition explained more than 90% of the variation in canopy reflectance as measured by imaging spectroscopy, indicating edaphic and compositional control of canopy chemical properties. We last found that soils explained between 30% and 70% of the variation in gap frequency in these forests, depending on the height threshold used to define gaps. Our findings indicate that a relatively small number of edaphic and compositional variables, corresponding to underlying geology, may be responsible for variations in canopy structure and chemistry over large expanses of Amazonian forest. PMID:25793602

Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

PubMed

Xiong, Wu; Zhao, Qingyun; Zhao, Jun; Xun, Weibing; Li, Rong; Zhang, Ruifu; Wu, Huasong; Shen, Qirong

2015-07-01

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

A Computer Code for Dynamic Stress Analysis of Media-Structure Problems with Nonlinearities (SAMSON). Volume III. User’s Manual.

DTIC Science & Technology

NONLINEAR SYSTEMS, LINEAR SYSTEMS, SUBROUTINES , SOIL MECHANICS, INTERFACES, DYNAMICS, LOADS(FORCES), FORCE(MECHANICS), DAMPING, ACCELERATION, ELASTIC...PROPERTIES, PLASTIC PROPERTIES, CRACKS , REINFORCING MATERIALS , COMPOSITE MATERIALS , FAILURE(MECHANICS), MECHANICAL PROPERTIES, INSTRUCTION MANUALS, DIGITAL COMPUTERS...STRESSES, *COMPUTER PROGRAMS), (*STRUCTURES, STRESSES), (*DATA PROCESSING, STRUCTURAL PROPERTIES), SOILS , STRAIN(MECHANICS), MATHEMATICAL MODELS

Use of reinforced soil foundation (RSF) to support shallow foundation : technical summary report, November 2008.

DOT National Transportation Integrated Search

2008-11-01

The presence of a weak soil supporting structural foundations results in low load bearing capacity and : excessive settlements, which can cause structural damage, reduction in durability, and/or deterioration in : performance level. Conventional trea...

Soil-structure interaction studies for understanding the behavior of integral abutment bridges.

DOT National Transportation Integrated Search

2012-03-01

Integral Abutment Bridges (IAB) are bridges without any joints within the bridge deck or between the : superstructure and the abutments. An IAB provides many advantages during construction and maintenance of : a bridge. Soil-structure interactions at...

Variation in Vegetation Structure and Soil Properties, and the Relation Between Understory Plants and Environmental Variables Under Different Phyllostachys pubescens Forests in Southeastern China

NASA Astrophysics Data System (ADS)

Zhang, Changshun; Xie, Gaodi; Fan, Shaohui; Zhen, Lin

2010-04-01

Biodiversity maintenance and soil improvement are key sustainable forestry objectives. Research on the effects of bamboo forest management on plant diversity and soil properties are therefore necessary in bamboo-growing regions, such as southeastern China’s Shunchang County, that have not been studied from this perspective. We analyzed the effects of different Phyllostachys pubescens proportions in managed forests on vegetation structure and soil properties using pure Cunninghamia lanceolata forests as a contrast, and analyzed the relation between understory plants and environmental variables (i.e., topography, stand and soil characteristics) by canonical correspondence analysis (CCA). The forest with 80% P. pubescens and 20% hardwoods (such as Phoebe bournei, Jatropha curcas, Schima superba) maintained the highest plant diversity and best soil properties, with significantly higher plant diversity than the C. lanceolata forest, and better soil physicochemical and biological properties. The distribution of understory plants is highly related to environmental factors. Silvicultural disturbance strongly influenced the ability of different bamboo forests to maintain biodiversity and soil quality under extensive management, and the forest responses to management were consistent with the intermediate-disturbance hypothesis (i.e., diversity and soil properties were best at intermediate disturbance levels). Our results suggest that biodiversity maintenance and soil improvement are important management goals for sustainable bamboo management. To achieve those objectives, managers should balance the inputs and outputs of nutrients and protect understory plants by using appropriate fertilizer (e.g., organic fertilizer), adjusting stand structure, modifying utilization model and the harvest time, and controlling the intensity of culms and shoots harvests.

Carbon stabilization and microbial growth in acidic mine soils after addition of different amendments for soil reclamation

NASA Astrophysics Data System (ADS)

Zornoza, Raúl; Acosta, Jose; Ángeles Muñoz, María; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

2016-04-01

The extreme soil conditions in metalliferous mine soils have a negative influence on soil biological activity and therefore on soil carbon estabilization. Therefore, amendments are used to increase organic carbon content and activate microbial communities. In order to elucidate some of the factors controlling soil organic carbon stabilization in reclaimed acidic mine soils and its interrelationship with microbial growth and community structure, we performed an incubation experiment with four amendments: pig slurry (PS), pig manure (PM) and biochar (BC), applied with and without marble waste (MW; CaCO3). Results showed that PM and BC (alone or together with MW) contributed to an important increment in recalcitrant organic C, C/N ratio and aggregate stability. Bacterial and fungal growths were highly dependent on pH and labile organic C. PS supported the highest microbial growth; applied alone it stimulated fungal growth, and applied with MW it stimulated bacterial growth. BC promoted the lowest microbial growth, especially for fungi, with no significant increase in fungal biomass. MW+BC increased bacterial growth up to values similar to PM and MW+PM, suggesting that part of the biochar was degraded, at least in short-term mainly by bacteria rather than fungi. PM, MW+PS and MW+PM supported the highest microbial biomass and a similar community structure, related with the presence of high organic C and high pH, with immobilization of metals and increased soil quality. BC contributed to improved soil structure, increased recalcitrant organic C, and decreased metal mobility, with low stimulation of microbial growth.

Stabilities of ant nests and their adjacent soils

NASA Astrophysics Data System (ADS)

Echezona, B. C.; Igwe, C. A.

2012-10-01

Nests habour ants and termites and protect them from harsh environmental conditions. The structural stabilities of nests were studied to ascertain their relative vulnerability to environmental stresses. Arboreal-ant nests were pried from different trees, while epigeous-termite nests were excavated from soil surface within the sample area. Soils without any visible sign of ant or termite activity were also sampled 6 m away from the nests as control. Laboratory analysis result showed that irrespective of the tree hosts, the aggregate stabilities of the ant nests were lower than those of the ground termite, with nests formed on Cola nitida significantly showing lower aggregate stability (19.7%) than other antnest structures. Clay dispersion ratio, moisture content, water stable aggregate class <0.25mm and sand mass were each negatively correlated with aggregate stability, while water stable aggregate class1.00-0.50 mm gave a positive correlation. Nest structures were dominated more by water stable aggregate class >2.00 mm but path analysis demonstrated that water stable aggregate class <0.25 mm contributed most to the higher aggregate stability of the termite nest than the other nest. Nest aggregates had greater structural stability compared to the control soil. The higher structural stability of termite nests over other nest and soil was considered a better adaptive mechanism against body desiccation.

The structure of bacterial communities in natural and anthropogenic brown forest soils of the Botanical Garden on Murav'eva-Amurskogo Peninsula

NASA Astrophysics Data System (ADS)

Kovaleva, G. V.; Dobrovol'Skaya, T. G.; Golovacheva, A. V.

2007-05-01

The microbiological characterization of the brown forest soils in the territory of the Botanical Garden-Institute of the Far East Division of the Russian Academy of Sciences in southern Primor’e is given. The high humus content and weakly acid reaction of these soils were shown to provide the optimal conditions for the development of bacteria. In the brown forest soils differing in the thickness of the humus horizons, all the ecologic-trophic groups of bacteria were present and the bacterial communities were highly diverse. The structure of the bacterial communities was identical in all the organomineral horizons of the soils and varied greatly by the seasons. In the anthropogenically disturbed soils, the share of corynebacteria, which are resistant to stress and capable of the destruction of xenobiotics, decreased.

Analysis of soils - Part II: Determination of oligosaccharides in soils by MALDI-time-of-flight mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schuerch, S.; Howald, M.; Schlunegger, U.P.

1995-12-31

Polysaccharides are the most abundant organic compounds in nature. Decomposition of plant and animal residues leads to a high polysaccharide content in soils. The decomposition of carbohydrates and subsequent mineralization of the products are part of the cycle of life on earth. In extracts of soils collected in the Valle Onsernone (Ticino, Switzerland), oligosaccharides of different size and structure have been identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The selected soils show identical climatic parameters and pedological factors, whereas the age of fallow land is the only varying factor. Identification and structure elucidation of the oligosaccharides is performedmore » by substrate-specific enzymatic hydrolysis. Moreover the appearance and the distribution of the oligosaccharides is correlated to soil genesis.« less

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but onlymore » in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Finally, combining such an approach with broader knowledge of thresholding behavior – here related to active layer depth – would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.« less

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

DOE PAGES

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben; ...

2017-09-28

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but onlymore » in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Finally, combining such an approach with broader knowledge of thresholding behavior – here related to active layer depth – would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.« less

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

NASA Astrophysics Data System (ADS)

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben; Crump, Alex R.; Chen, Xingyuan; Hess, Nancy

2017-09-01

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but only in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Combining such an approach with broader knowledge of thresholding behavior - here related to active layer depth - would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.

Contributions of root and shoot derived-C to soil organic matter throughout an agricultural soil profile assessed by compound-specific 13C analysis

NASA Astrophysics Data System (ADS)

Mendez-Millan, Mercedes; Dignac, Marie-France; Rumpel, Cornelia; Rasse, Daniel P.; Derenne, Sylvie

2010-05-01

The turnover of soil organic matter (SOM) is generally studied in the topsoil horizons, where the highest concentrations of organic carbon (OC) are found. Subsoils, although containing lower amounts of organic carbon compared to topsoils, greatly contribute to the total carbon stocks within a soil profile. An increase in SOM aliphaticity was observed during SOM degradation, and also down the soil profile, suggesting that the stable pool of SOM is enriched in aliphatic structures. These alkyl-C structures might mainly derive from cutins and suberins, two biomacromolecules, which contain biomarkers specific for shoot and root plant biomass. The aim of this study was to use cutin and suberin structural units to follow the incorporation of plant biomass originating from roots and shoots throughout an agricultural soil profile. We measured the 13C natural abundance of root and shoot biomarkers in samples taken from 15 to 105 cm depth in a C3/C4 chronosequence. After 9 years of maize (C4) cropping, the distribution of root biomarkers (diacids) significantly changed and their concentration increased compared to the wheat (CC3) soil. The largest increase was observed at 60-75 cm where diacids reached up to 134 ?g/gOC compared to 23 ?g/gOC in the wheat soil. Higher inputs from maize root biomass are also suggested by an average 13C enrichment of the root markers in the maize compared to the wheat soil.

[Population structure of soil arthropod in different age Pinus massoniana plantations].

PubMed

Tan, Bo; Wu, Fu-zhong; Yang, Wan-qin; Zhang, Jian; Xu, Zhen-feng; Liu, Yang; Gou, Xiao-lin

2013-04-01

An investigation was conducted on the population structure of soil arthropod community in the 3-, 8-, 14-, 31-, and 40-years old Pinus massoniana plantations in the upper reaches of the Yangtze River in spring (May) and autumn (October), 2011, aimed to search for the scientific management of the plantation. A total of 4045 soil arthropods were collected, belonging to 57 families. Both the individual density and the taxonomic group number of the soil arthropod community decreased obviously with increasing soil depth, and this trend increased with increasing stand age. The dominant groups and ordinary groups of the soil arthropod community varied greatly with the stand age of P. massoniana plantation, and a significant difference (P<0.05) was observed in the individual density and taxonomic group number among different age P. massoniana plantations. In comparison with other stand age P. massoniana plantations, 3years old P. massoniana plantation had a significant difference in the structure and diversity of soil arthropod community, and the similarity index of the soil arthropod community was lower. The individual density, taxonomic group number, and diversity of soil arthropod community were the highest in 8-years old P. massoniana plantation, and then, decreased obviously with increasing stand age. It was suggested that the land fertility of the P. massoniana plantations could be degraded with increasing stand age, and it would be appropriate to make artificial regulation and restoration in 8-years old P. massoniana plantation.

Current advancements and challenges in soil-root interactions modelling

NASA Astrophysics Data System (ADS)

Schnepf, Andrea; Huber, Katrin; Abesha, Betiglu; Meunier, Felicien; Leitner, Daniel; Roose, Tiina; Javaux, Mathieu; Vanderborght, Jan; Vereecken, Harry

2015-04-01

Roots change their surrounding soil chemically, physically and biologically. This includes changes in soil moisture and solute concentration, the exudation of organic substances into the rhizosphere, increased growth of soil microorganisms, or changes in soil structure. The fate of water and solutes in the root zone is highly determined by these root-soil interactions. Mathematical models of soil-root systems in combination with non-invasive techniques able to characterize root systems are a promising tool to understand and predict the behaviour of water and solutes in the root zone. With respect to different fields of applications, predictive mathematical models can contribute to the solution of optimal control problems in plant recourse efficiency. This may result in significant gains in productivity, efficiency and environmental sustainability in various land use activities. Major challenges include the coupling of model parameters of the relevant processes with the surrounding environment such as temperature, nutrient concentration or soil water content. A further challenge is the mathematical description of the different spatial and temporal scales involved. This includes in particular the branched structures formed by root systems or the external mycelium of mycorrhizal fungi. Here, reducing complexity as well as bridging between spatial scales is required. Furthermore, the combination of experimental and mathematical techniques may advance the field enormously. Here, the use of root system, soil and rhizosphere models is presented through a number of modelling case studies, including image based modelling of phosphate uptake by a root with hairs, model-based optimization of root architecture for phosphate uptake from soil, upscaling of rhizosphere models, modelling root growth in structured soil, and the effect of root hydraulic architecture on plant water uptake efficiency and drought resistance.

Current Advancements and Challenges in Soil-Root Interactions Modelling

NASA Astrophysics Data System (ADS)

Schnepf, A.; Huber, K.; Abesha, B.; Meunier, F.; Leitner, D.; Roose, T.; Javaux, M.; Vanderborght, J.; Vereecken, H.

2014-12-01

Roots change their surrounding soil chemically, physically and biologically. This includes changes in soil moisture and solute concentration, the exudation of organic substances into the rhizosphere, increased growth of soil microorganisms, or changes in soil structure. The fate of water and solutes in the root zone is highly determined by these root-soil interactions. Mathematical models of soil-root systems in combination with non-invasive techniques able to characterize root systems are a promising tool to understand and predict the behaviour of water and solutes in the root zone. With respect to different fields of applications, predictive mathematical models can contribute to the solution of optimal control problems in plant recourse efficiency. This may result in significant gains in productivity, efficiency and environmental sustainability in various land use activities. Major challenges include the coupling of model parameters of the relevant processes with the surrounding environment such as temperature, nutrient concentration or soil water content. A further challenge is the mathematical description of the different spatial and temporal scales involved. This includes in particular the branched structures formed by root systems or the external mycelium of mycorrhizal fungi. Here, reducing complexity as well as bridging between spatial scales is required. Furthermore, the combination of experimental and mathematical techniques may advance the field enormously. Here, the use of root system, soil and rhizosphere models is presented through a number of modelling case studies, including image based modelling of phosphate uptake by a root with hairs, model-based optimization of root architecture for phosphate uptake from soil, upscaling of rhizosphere models, modelling root growth in structured soil, and the effect of root hydraulic architecture on plant water uptake efficiency and drought resistance.

Influence of crop rotation and tillage intensity on soil physical properties and functions

NASA Astrophysics Data System (ADS)

Krümmelbein, Julia

2013-04-01

Soil tillage intensity can vary concerning tillage depth, frequency, power input into the soil and degree of soil turn-over. Conventional tillage systems where a plough is regularly used to turn over the soil can be differentiated from reduced tillage systems without ploughing but with loosening the upper soil and no tillage systems. Between conventional tillage and no tillage is a wide range of more or less reduced tillage systems. In our case the different tillage intensities are not induced by different agricultural machinery or techniques, but result from varying crop rotations with more or less perennial crops and therefore lower or higher tillage frequency. Our experimental area constitutes of quite unstructured substrates, partly heavily compacted. The development of a functioning soil structure and accumulation of nutrients and organic matter are of high importance. Three different crop rotations induce varying tillage intensities and frequencies. The first crop rotation (Alfalfa monoculture) has only experienced seed bed preparation once and subsequently is wheeled once a year to cut and chaff the biomass. The second crop rotation contains perennial and annual crops and has therefore been tilled more often, while the third crop rotation consists only of annual crops with annual seedbed preparation. Our results show that reduced tillage intensity/frequency combined with the intense root growth of Alfalfa creates the most favourable soil physical state of the substrate compared to increased tillage and lower root growth intensity of the other crop rotations. Soil tillage disturbs soil structure development, especially when the substrate is mechanically unstable as in our case. For such problematic locations it is recommendable to reduce tillage intensity and/or frequency to allow the development of soil structure enhanced by root growth and thereby the accumulation of organic matter and nutrients within the rooting zone.

A soil alteration index based on phospholipid fatty acids.

PubMed

Puglisi, Edoardo; Nicelli, Marco; Capri, Ettore; Trevisan, Marco; Del Re, Attilio A M

2005-12-01

Phospholipid fatty acid (PLFA) analysis has gained great importance in the study of soil microbial community structure. This structure can give indication of the soil status. Purpose of the present paper is to analyse PLFA patterns in altered agricultural soils in order to develop a soil status alteration index. Soils subjected either to intensive agricultural exploitation, or to overflow by municipal and industrial wastes, or to irrigation with saline waters were analysed for PLFA content and compared to adjacent untreated soils by means of different statistical techniques. Principal component analysis separated PLFAs in three groups: unsaturated PLFAs (first axis, 48% of total variance), monounsaturated and cyclopropane PLFAs (second axis, 28% of total variance) and polyunsaturated PLFAs (third axis, 24% of total variance). By means of canonical discriminant analysis, a soil alteration index (SAI) was produced from 15 PLFAs using two data sets. A third data set was used to test the SAI general validity together with other data sets reported in literature. The index validity was confirmed in most cases: SAI gave higher scores for control soils and was generally able to classify soils according to their reported degree of alteration.

Dynamic changes of bacterial community under bioremediation with Sphingobium sp. LY-6 in buprofezin-contaminated soil.

PubMed

Liu, Yuan; Hou, Qianqian; Liu, Wanru; Meng, Yawen; Wang, Guangli

2015-08-01

Buprofezin is a commonly used chemical with satisfactory biological activity against sucking insect pests, but its disposal can cause serious environmental problems. To study the feasibility of remedying contamination by buprofezin, microcosm experiments were carried out to study the effects of various concentrations of buprofezin and Sphingobium sp. LY-6 on soil bacterial communities in soils collected from vegetable fields. In this experiment, the results showed that buprofezin was effectively degraded by Sphingobium sp. LY-6 in incubation soils. Comparing to non-incubated soils, the cumulative degradation ratio of buprofezin was significantly increased, up to the extent of 85 and 51%, in the initial concentration of 10 and 100 mg kg(-1). The abundance and community structure of the bacterial communities were analysed by real-time PCR (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The findings suggest that buprofezin had a negative effect on soil bacterial community, and decreases in bacterial abundance were observed in the later part of the incubation period. The bacterial community structure and diversity shifted significantly at each sampling time. In conclusion, the buprofezin-degrading strain LY-6 played a major role in the bioremediation of the buprofezin-contaminated soil and influenced the dynamics and structure of the bacterial community, demonstrating the great potential of exogenous microorganisms for soil remediation.

Nematodes as bioindicators of soil degradation due to heavy metals.

PubMed

Šalamún, Peter; Renčo, Marek; Kucanová, Eva; Brázová, Tímea; Papajová, Ingrid; Miklisová, Dana; Hanzelová, Vladimíra

2012-11-01

The effect of distance from a heavy metal pollution source on the soil nematode community was investigated on four sampling sites along an 4 km transect originating at the Kovohuty a.s. Krompachy (pollution source). The soil nematode communities were exposed to heavy metal influence directly and through soil properties changes. We quantified the relative effects of total and mobile fraction of metals (As, Cd, Cr, Cu, Pb, and Zn) on soil ecosystem using the nematode community structure (trophic and c-p groups,) and ecological indices (Richness of genera, H', MI2-5, etc.). Pollution effects on the community structure of soil free living nematodes was found to be the highest near the pollution source, with relatively low population density and domination of insensitive taxa. A decrease in heavy metals contents along the transect was linked with an increase in complexity of nematode community. The majority of used indices (MI2-5, SI, H') negatively correlated (P < 0.05 or P < 0.01) with heavy metals content and were sensitive to soil ecosystem disturbance. Contamination by heavy metals has negatively affected the soil environment, which resulted in nematode community structure and ecological indices changes. Results showed that the free-living nematodes are useful tools for bioindication of contamination and could be used as an alternative to the common approaches based on chemical methods.

Dynamics of Verticillium species microsclerotia in field soils in response to fumigation, cropping patterns, and flooding

USDA-ARS?s Scientific Manuscript database

Many soil-inhabiting fungi are capable of surviving the dynamic soil microenvironment through the formation of resilient resting structures, such as thick-walled spores, melanized hyphae, and sclerotia. Verticillium dahliae is a soil-inhabiting, economically significant plant pathogenic fungus that ...

Retention of Nickel in Soils: Sorption-Desorption and Extended X-ray Absorption Fine Structure Experiments

EPA Science Inventory

Adsorption and desorption of heavy metals in soils are primary factors that influence their bioavailability and mobility in the soil profile. To examine the characteristics of nickel (Ni) adsorption-desorption in soils, kinetic batch experiments were carried out followed by Ni re...

Impacts of deficit irrigation and altered rooting patterns on soil structure and associated soil properties

USDA-ARS?s Scientific Manuscript database

A better understanding of belowground systems and overall management impacts on soil health is needed to improve crop production and long-term sustainability under deficit irrigation. This study investigates effects of deficit irrigation on rooting patterns in maize and subsequent impacts on soil pr...

Patterns of soil community structure differ by scale and ecosystem type along a large-scale precipitation gradient

USDA-ARS?s Scientific Manuscript database

Climate models predict increased variability in precipitation regimes, which will likely increase frequency/duration of drought. Reductions in soil moisture affect physical and chemical characteristics of the soil habitat and can influence soil organisms such as mites and nematodes. These organisms ...

Soil microbial community structure and target organisms under different fumigation treatments

USDA-ARS?s Scientific Manuscript database

Several high-value crop producers in California rely heavily on soil fumigants to control key diseases, nematodes, weeds and volunteer crops. Fumigants with broad biocidal activity can affect both target and non-target soil organisms. The ability of non-target soil organisms to recover after fumigat...

Soil physical conditions as livestock treading effect in tropical Agroecosystem of dryland and strategies to mitigate desertification risk

NASA Astrophysics Data System (ADS)

Florentino, A.; Torres, D.; Ospina, A.; Contreras, J.; Palma, Z.; Silvera, J.

2012-04-01

Soil degradation in natural ecosystem of arid and semi-arid zones of Venezuela due to livestock treading (goats) it is an important problem that affect their environment functions; increase soil erodibility, bulk density, water losses and reduce porosity, water infiltration rate and soil structural stability. The presence of biological crust (BSC) in this type of soil it is very common. The objective of this study was to evaluate the soil surface physical quality through the use of selected indicators, mainly some of that related to structural stability, infiltrability and the prediction of soil erosion risk in two zones of Lara state: 1) Quíbor (QUI) and 2) Humocaro Bajo (HB). The study was conducted on two selected plots (30 m x 20 m) in each zone, with natural vegetation and BSC cover, with areas affected by different degree of compaction due to treading in the paths where the goats are moving. Five sites per plot (50 cm x 50 cm) under vegetation cover and five sites over the path with bare soil were sampled (0-7,5 and 7,5-15 cm depth). The results showed that soil macroaggregate stability (equivalent diameter of aggregates >0,25 mm) was significantly higher (p<0,05 %) in soil with vegetation cover and BSC compared with bare soil. Sealing index, as a measure of aggregate stability, determined in laboratory under simulated rain and expressed as hydraulic conductivity of soil surface sealing (Kse), decreased with decreasing soil vegetation cover and the presence of BSC. However, Ksei (i: inicial) and Ksef (f: final) were significantly greater in soil with more than 75 % of BSC in comparison to bare soils. The sealing index it is used to for to estimate changes in soil water losses. As the sealing index increases, the susceptibility of the soil to undergo surface sealing or slaking decrease. These results suggested that soil physical properties are potential indicators of soil quality with regard to soil erodibility and showed that soils under vegetation cover had higher quality level than bare soils. Some predictive regression equation had a high R2 value and was a useful tool for to evaluate the risk of extreme climatic changes and to mitigate their detrimental effects. We conclude that the global climatic change (CCG) will have a negative effect on these agroecosystems functions, mainly in soil and water conservation, carbon sequestration, and productivity. Natural recovery of soil physical properties from treading damage of pastoral soils will be possible in the future with the implementation of soil management strategies, mainly through re-vegetation and recuperation of the BSC. Key word: Soil structure; aggregate stability; soil sealing index; hydraulic conductivity of surface sealing.

Using operational and defined fractions to assess soil organic matter stabilization and structure

NASA Astrophysics Data System (ADS)

Horwath, W. R.

2015-12-01

Studies on soil organic matter (SOM) began with alkaline solvents revealing a dark colored substance that could be isolated under low pH. Further studies revealed fulvic and humic acids and humin fractions leading to theories on functional groups and metal-clay bridging mechanisms. The fate of isotopes in these fractions revealed soil carbon pools with varying turnover rates with half the soil carbon (C) in humin and acid hydrolyzed fractions over 1000 years old. These results are the basis of the three pool conceptual framework used in many biogeochemical models. Theories on the role of functional groups and compound classes further elaborated concepts on physical (aggregates) and chemical mechanisms of C stabilization. With the advance of analytical instrumentation, the operational fractions were further defined to the compound and molecular levels. These studies confirmed the majority of soil C is microbially derived. Our observation that all microbial groups contributed nonselectively to soil C maintenance independent of mineralogy suggests that compound characteristics within integrated structures are more important than the source of individual compounds for stabilizing soil C. In dissolved organic C floccing studies using Near Edge X-ray Fine Structure analysis, we found that aromatic compounds interacted first with Fe, however, the majority of direct bonds to Fe were polysaccharides, reinforcing that an integrative chemical structure rather than direct bonds imparted stability in organo-metal interactions. Using a novel differential scanning calorimeter coupled to an isotope ratio mass spectrometer setup, we confirmed that the presence of clays (independent of clay type) increased the microbial utilization of calcium stabilized high versus low temperature compounds, asserting that higher temperature compounds (i.e., phenolics) are likely less tightly bound by clay minerals. The integration of operational and defined fractions of SOM remains a legitimate approach to examine SOM structure and stabilization across scales of soil development and management.

Soil factors involved in the diversity and structure of soil bacterial communities in commercial organic olive orchards in Southern Spain.

PubMed

Landa, B B; Montes-Borrego, M; Aranda, S; Soriano, M A; Gómez, J A; Navas-Cortés, J A

2014-04-01

Nowadays, there is a tendency in olive production systems to reduce tillage or keep a vegetative cover to reduce soil erosion and degradation. However, there is scarce information on the effects of different soil management systems (SMS) in soil bacterial community composition of olive groves. In this study, we have evaluated the effects of soil type and different SMS implemented to control weeds in the structure and diversity of bacterial communities of 58 soils in the two geographic areas that best represent the organic olive production systems in Spain. Bacterial community composition assessed by frequency and intensity of occurrence of terminal restriction profiles (TRFs) derived from terminal restriction fragment length polymorphism (T-RFLP) analysis of amplified 16S ribosomal deoxyribonucleic acid were strongly correlated with soil type/field site (Eutric/Calcaric) that differed mainly in soil particle size distribution and soil pH, followed by a strong effect of SMS, in that order. Canonical discriminant (CD) analysis of TRFs properly classified all of the olive orchard soils as belonging to their respective soil type or SMS. Furthermore, only a small set of TRFs were enough to clearly and significantly differentiate soil samples according to soil type or SMS. Those specific TRFs could be used as bioindicators to assess the effect of changes in SMS aimed to enhance soil quality in olive production systems. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition.

PubMed

Ma, Xingyu; Zhao, Cancan; Gao, Ying; Liu, Bin; Wang, Tengxu; Yuan, Tong; Hale, Lauren; Nostrand, Joy D Van; Wan, Shiqiang; Zhou, Jizhong; Yang, Yunfeng

2017-08-01

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling. © 2017 John Wiley & Sons Ltd.

The Exotic Legume Tree Species Acacia holosericea Alters Microbial Soil Functionalities and the Structure of the Arbuscular Mycorrhizal Community▿

PubMed Central

Remigi, P.; Faye, A.; Kane, A.; Deruaz, M.; Thioulouse, J.; Cissoko, M.; Prin, Y.; Galiana, A.; Dreyfus, B.; Duponnois, R.

2008-01-01

The response of microbial functional diversity as well as its resistance to stress or disturbances caused by the introduction of an exotic tree species, Acacia holosericea, ectomycorrhized or not with Pisolithus albus, was examined. The results show that this ectomycorrhizal fungus promotes drastically the growth of this fast-growing tree species in field conditions after 7 years of plantation. Compared to the crop soil surrounding the A. holosericea plantation, this exotic tree species, associated or not with the ectomycorrhizal symbiont, induced strong modifications in soil microbial functionalities (assessed by measuring the patterns of in situ catabolic potential of microbial communities) and reduced soil resistance in response to increasing stress or disturbance (salinity, temperature, and freeze-thaw and wet-dry cycles). In addition, A. holosericea strongly modified the structure of arbuscular mycorrhizal fungus communities. These results show clearly that exotic plants may be responsible for important changes in soil microbiota affecting the structure and functions of microbial communities. PMID:18203858

Multivariate functions for predicting the sorption of 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5-tricyclohexane (RDX) among taxonomically distinct soils.

PubMed

Katseanes, Chelsea K; Chappell, Mark A; Hopkins, Bryan G; Durham, Brian D; Price, Cynthia L; Porter, Beth E; Miller, Lesley F

2016-11-01

After nearly a century of use in numerous munition platforms, TNT and RDX contamination has turned up largely in the environment due to ammunition manufacturing or as part of releases from low-order detonations during training activities. Although the basic knowledge governing the environmental fate of TNT and RDX are known, accurate predictions of TNT and RDX persistence in soil remain elusive, particularly given the universal heterogeneity of pedomorphic soil types. In this work, we proposed a new solution for modeling the sorption and persistence of these munition constituents as multivariate mathematical functions correlating soil attribute data over a variety of taxonomically distinct soil types to contaminant behavior, instead of a single constant or parameter of a specific absolute value. To test this idea, we conducted experiments measuring the sorption of TNT and RDX on taxonomically different soil types that were extensively physical and chemically characterized. Statistical decomposition of the log-transformed, and auto-scaled soil characterization data using the dimension-reduction technique PCA (principal component analysis) revealed a strong latent structure based in the multiple pairwise correlations among the soil properties. TNT and RDX sorption partitioning coefficients (KD-TNT and KD-RDX) were regressed against this latent structure using partial least squares regression (PLSR), generating a 3-factor, multivariate linear functions. Here, PLSR models predicted KD-TNT and KD-RDX values based on attributes contributing to endogenous alkaline/calcareous and soil fertility criteria, respectively, exhibited among the different soil types: We hypothesized that the latent structure arising from the strong covariance of full multivariate geochemical matrix describing taxonomically distinguished soil types may provide the means for potentially predicting complex phenomena in soils. The development of predictive multivariate models tuned to a local soil's taxonomic designation would have direct benefit to military range managers seeking to anticipate the environmental risks of training activities on impact sites. Published by Elsevier Ltd.

Influence of management history and landscape variables on soil organic carbon and soil redistribution

USGS Publications Warehouse

Venteris, E.R.; McCarty, G.W.; Ritchie, J.C.; Gish, T.

2004-01-01

Controlled studies to investigate the interaction between crop growth, soil properties, hydrology, and management practices are common in agronomy. These sites (much as with real world farmland) often have complex management histories and topographic variability that must be considered. In 1993 an interdisiplinary study was started for a 20-ha site in Beltsville, MD. Soil cores (271) were collected in 1999 in a 30-m grid (with 5-m nesting) and analyzed as part of the site characterization. Soil organic carbon (SOC) and 137Cesium (137Cs) were measured. Analysis of aerial photography from 1992 and of farm management records revealed that part of the site had been maintained as a swine pasture and the other portion as cropped land. Soil properties, particularly soil redistribution and SOC, show large differences in mean values between the two areas. Mass C is 0.8 kg m -2 greater in the pasture area than in the cropped portion. The pasture area is primarily a deposition site, whereas the crop area is dominated by erosion. Management influence is suggested, but topographic variability confounds interpretation. Soil organic carbon is spatially structured, with a regionalized variable of 120 m. 137Cs activity lacks spatial structure, suggesting disturbance of the profile by animal activity and past structures such as swine shelters and roads. Neither SOC nor 137Cs were strongly correlated to terrain parameters, crop yields, or a seasonal soil moisture index predicted from crop yields. SOC and 137Cs were weakly correlated (r2 ???0.2, F-test P-value 0.001), suggesting that soil transport controls, in part, SOC distribution. The study illustrates the importance of past site history when interpreting the landscape distribution of soil properties, especially those strongly influenced by human activity. Confounding variables, complex soil hydrology, and incomplete documentation of land use history make definitive interpretations of the processes behind the spatial distributions difficult. Such complexity may limit the accuracy of scaling approaches to mapping SOC and soil redistribution.

Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations

NASA Astrophysics Data System (ADS)

Zhou, Xiaoqi; Guo, Zhiying; Chen, Chengrong; Jia, Zhongjun

2017-04-01

Forest plantations have been recognised as a key strategy management tool for stocking carbon (C) in soils, thereby contributing to climate warming mitigation. However, long-term ecological consequences of anthropogenic forest plantations on the community structure and diversity of soil microorganisms and the underlying mechanisms in determining these patterns are poorly understood. In this study, we selected 78-year-old tree plantations that included three coniferous tree species (i.e. slash pine, hoop pine and kauri pine) and a eucalypt species in subtropical Australia. We investigated the patterns of community structure, and the diversity of soil bacteria and eukaryotes by using high-throughput sequencing of 16S rRNA and 18S rRNA genes. We also measured the potential methane oxidation capacity under different tree species. The results showed that slash pine and Eucalyptus significantly increased the dominant taxa of bacterial Acidobacteria and the dominant taxa of eukaryotic Ascomycota, and formed clusters of soil bacterial and eukaryotic communities, which were clearly different from the clusters under hoop pine and kauri pine. Soil pH and nutrient quality indicators such as C : nitrogen (N) and extractable organic C : extractable organic N were key factors in determining the patterns of soil bacterial and eukaryotic communities between the different tree species treatments. Slash pine and Eucalyptus had significantly lower soil bacterial and eukaryotic operational taxonomical unit numbers and lower diversity indices than kauri pine and hoop pine. A key factor limitation hypothesis was introduced, which gives a reasonable explanation for lower diversity indices under slash pine and Eucalyptus. In addition, slash pine and Eucalyptus had a higher soil methane oxidation capacity than the other tree species. These results suggest that significant changes in soil microbial communities may occur in response to chronic disturbance by tree plantations, and highlight the importance of soil pH and physiochemical characteristics in microbially mediated ecological processes in forested soils.

Structural quality of on Oxisol in recovery for 18 years

NASA Astrophysics Data System (ADS)

dos Santos Batista Bonini, C.; Alves, M. C.; Marchini, D. C.; Garcia de Arruda, O.; Nilce Souto Filho, S.

2012-04-01

Incorrect use of soil and large buildings construction in rural areas are causing changes to it, making them less productive and thus increasing the degraded areas. Techniques aimed at ecological restoration of degraded soils have been investigated. In this sense we investigated the positive changes in the structural quality of a soil that was beheaded in human intervention techniques for recovery for 18 years, having been used green manures, gypsum and pasture. The studied area is located in Mato Grosso do Sul, Brazil. The experimental design was a completely randomized with seven treatments and four replications. The treatments were: control (tilled soil without culture); Stizolobium aterrium; Cajanus cajan; lime+S. aterrimum; lime+C. cajan; lime+gypsum+S. aterrimum; lime+gypsum+C. cajan. In 1994, all treatments with C. cajan were replaced by Canavalia ensiformis and in 1999, Brachiaria decumbens was implanted in all treatments. Data from vegetated treatments were compared with the control bare soil and native vegetation (savannah). We evaluated the distribution and aggregate stability in water, soil samples were collected in 2010 in the depths: 0.00-0.10; 0.10-0.20 and 0,20-0.40 m. The results were analyzed by analysis of variance, following Scott-Knott test (5%) of probability to compare averages. Evaluating the results is noted that in the depth of 0.00-0.10 m, the control bare soil and savannah soil had lower and higher DMP, respectively. All recovery treatments were DMP greater than found for the bare soil control. Treatments: S. aterrimum, lime + gypsum + C. cajan and lime + gypsum + S. aterrimum and the savannah control were similar in the depth of 0.00-0.10 m. All of the recovery treatment in the depth from 0.00-0.10 m with values is close to the native vegetation of the savannah. Depths of 0.10-0.20 and 0.20-0.40 m results obtained for DMP treatments in recovery are similar to the bare soil, except for treatments with S. aterrimum and lime + gypsum + S. aterrimum that had values were similar to the savannah control. This behavior shows that the recovery of soil treatments were eficient only the superficial layer soil and other depths in the structure is still in recovery. It is concluded that the recovery treatment have positively influenced the structure quality in the 0.00-0.10 m depth : the recovery treatment with S. aterrimum and lime + gypsum + S. aterrimum were the most promising in the recovery structural quality.

ORGANIC VS CONVENTIONAL: SOIL NEMATODE COMMUNITY STRUCTURE AND FUNCTION.

PubMed

Kapp, C; Storey, S G; Malan, A P

2014-01-01

Global increases in human population are creating an ever-greater need for food production. Poor soil management practices have degraded soil to such an extent that rapidly improved management practices is the only way to ensure future food demands. In South Africa, deciduous fruit producers are realising the need for soil health, and for an increased understanding of the benefits of soil ecology, to ensure sustainable fruit production. This depends heavily on improved orchard management. Conventional farming relies on the addition of artificial fertilizers, and the application of chemicals, to prevent or minimise, the effects of the soil stages of pest insects, and of plant-parasitic nematodes. Currently, there is resistance toward conventional farming practices, which, it is believed, diminishes biodiversity within the soil. The study aimed to establish the soil nematode community structure and function in organically, and conventionally, managed deciduous fruit orchards. This was done by determining the abundance, the diversity, and the functionality of the naturally occurring free-living, and plant-parasitic, nematodes in deciduous fruit orchards in the Western Cape province of South Africa. The objective of the study was to form the basis for the use of nematodes as future indicators of soil health in deciduous fruit orchards. Orchards from neighbouring organic, and conventional, apricot farms, and from an organic apple orchard, were studied. All the nematodes were quantified, and identified, to family level. The five nematode-classified trophic groups were found at each site, while 14 families were identified in each orchard, respectively. Herbivores were dominant in all the orchards surveyed. Organic apples had the fewest herbivores and fungivores, with the highest number of carnivores. When comparing organic with conventional apricot orchards, higher numbers of plant-parasitic nematodes were found in the organic apricot orchards. The Maturity Index (MI) indicated that all orchard soils had values below 1.5, indicating disturbed conditions. The conventionally managed apricot orchard had the highest MI value, of 1.48. The Plant Parasitic Index (PPI) value was highest in the organically managed apricot orchard. In order to determine the existing enrichment, structural, and basal conditions, the nematode faunal analysis was applied to each site. All the sites indicated enriched and structured conditions. Regarding the diversity, the richness, and the evenness of the distribution, soil from the conventional apricot orchard had the highest species richness, whereas the organic apple orchard soil had the most even distribution of families. Different management practices in fruit orchards did not show marked differences in terms of community composition and structure.

Evaluation of soil-foundation-structure interaction effects on seismic response demands of multi-story MRF buildings on raft foundations

NASA Astrophysics Data System (ADS)

Abdel Raheem, Shehata E.; Ahmed, Mohamed M.; Alazrak, Tarek M. A.

2015-03-01

Soil conditions have a great deal to do with damage to structures during earthquakes. Hence the investigation on the energy transfer mechanism from soils to buildings during earthquakes is critical for the seismic design of multi-story buildings and for upgrading existing structures. Thus, the need for research into soil-structure interaction (SSI) problems is greater than ever. Moreover, recent studies show that the effects of SSI may be detrimental to the seismic response of structure and neglecting SSI in analysis may lead to un-conservative design. Despite this, the conventional design procedure usually involves assumption of fixity at the base of foundation neglecting the flexibility of the foundation, the compressibility of the underneath soil and, consequently, the effect of foundation settlement on further redistribution of bending moment and shear force demands. Hence the SSI analysis of multi-story buildings is the main focus of this research; the effects of SSI are analyzed for typical multi-story building resting on raft foundation. Three methods of analysis are used for seismic demands evaluation of the target moment-resistant frame buildings: equivalent static load; response spectrum methods and nonlinear time history analysis with suit of nine time history records. Three-dimensional FE model is constructed to investigate the effects of different soil conditions and number of stories on the vibration characteristics and seismic response demands of building structures. Numerical results obtained using SSI model with different soil conditions are compared to those corresponding to fixed-base support modeling assumption. The peak responses of story shear, story moment, story displacement, story drift, moments at beam ends, as well as force of inner columns are analyzed. The results of different analysis approaches are used to evaluate the advantages, limitations, and ease of application of each approach for seismic analysis.

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

PubMed Central

Singh, Baneshwar; Minick, Kevan J.; Strickland, Michael S.; Wickings, Kyle G.; Crippen, Tawni L.; Tarone, Aaron M.; Benbow, M. Eric; Sufrin, Ness; Tomberlin, Jeffery K.; Pechal, Jennifer L.

2018-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3–732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences. PMID:29354106

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function.

PubMed

Singh, Baneshwar; Minick, Kevan J; Strickland, Michael S; Wickings, Kyle G; Crippen, Tawni L; Tarone, Aaron M; Benbow, M Eric; Sufrin, Ness; Tomberlin, Jeffery K; Pechal, Jennifer L

2017-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3-732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem function surrounding carrion decomposition islands and can be applicable to environmental bio-monitoring and forensic sciences.

The engineering significance of shrinkage and swelling soils in blast damage investigations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vitton, S.J.; Harris, W.W.

1996-12-01

In the US each year it has been estimated that expansive soils cause approximately $9.0 billion in damage to buildings, roads, airports, and other facilities. This figure alone exceeds the damage estimate for earthquakes, floods, tornadoes, and hurricanes combined. Unfortunately, some cases of expansive soil damage (swelling) are blamed on rock blasting operations if the blasting operations are located within the immediate area. While simple tests, such as the Atterberg limits test, can characterize a soil as expansive, it does not necessarily answer the question whether the foundation soils are causing distresses to a structure. In particular, it appears thatmore » once a soil has been labeled as nonexpansive it is no longer considered as a problem soil, in which case blast vibrations become the prime suspect. It should be emphasized, however, that even non-plastic soils, those soils with low to nonexistent plastic indexes, can exhibit significant shrinkage characteristics that can result in significant damage to structures. While expansive soil is a function of the mineralogy of the soil particles, i.e., swelling clay minerals, shrinkage is caused by the loss of moisture from soil as capillary pressures exceed the cohesion or tensile strength and is therefore a function of the soils particle size and its pore size distribution. This is a significant problem for all fine grained soils regardless of the soil`s mineralogy. It`s particularly important for regions of the US that typically have a positive water balance but experience significant drought periods when soil moisture is lost.« less

Evaluating Brazilian sugarcane expansion effects on soil structure using VESS

USDA-ARS?s Scientific Manuscript database

Increasing global demand for biofuel has accelerated land-use change (LUC) in Brazil, primarily by replacing degraded pasture with sugarcane (Saccharum officinarum). The intensive echanization associated with this LUC has increased concerns regarding soil structural quality (SSQ). Through decades of...

Development of an earth pressure model for design of earth retaining structures in piedmont soil.

DOT National Transportation Integrated Search

2008-10-01

Anecdotal evidence suggests that earth pressure in Piedmont residual soils is typically over estimated. Such estimates of earth pressure impact the design of earth retaining structures used on highway projects. Thus, the development of an appropriate...

Evaluation of structure from motion for soil microtopography measurement

USDA-ARS?s Scientific Manuscript database

Recent developments in low cost structure from motion (SFM) technologies offer new opportunities for geoscientists to acquire high resolution soil microtopography data at a fraction of the cost of conventional techniques. However, these new methodologies often lack easily accessible error metrics an...

Changes in Soil Microbial Community Structure with Flooding

USDA-ARS?s Scientific Manuscript database

Flooding disturbs both above- and below-ground ecosystem processes. Although often ignored, changes in below-ground environments are no less important than those that occur above-ground. Shifts in soil microbial community structure are expected when anaerobic conditions develop from flooding. The ...

Geophysical Methods for Monitoring Soil Stabilization Processes

EPA Science Inventory

Soil stabilization involves methods used to turn unconsolidated and unstable soil into a stiffer, consolidated medium that could support engineered structures, alter permeability, change subsurface flow, or immobilize contamination through mineral precipitation. Among the variety...

Impact of endochitinase-transformed white spruce on soil fungal communities under greenhouse conditions.

PubMed

Lamarche, Josyanne; Stefani, Franck O P; Séguin, Armand; Hamelin, Richard C

2011-05-01

Chitinase genes isolated from plants, bacteria or fungi have been widely used in genetic engineering to enhance the resistance of crops and trees to fungal pathogens. However, there are concerns about the possible effect of chitinase-transformed plants on nontarget fungi. This study aimed at evaluating the impact of endochitinase-transformed white spruce on soil fungal communities. Endochitinase-expressing white spruce and untransformed controls were transplanted in soils from two natural forests and grown for 8 months in a greenhouse. Soil fungal biomass and diversity, estimated through species richness and Shannon and Rao diversity indices, were not different between transgenic and control tree rhizospheres. The fungal phylogenetic community structure was the same in soil samples from control and transgenic white spruces after 8 months. Soil type and presence of seedlings had a much more significant impact on fungal community structure than the insertion and expression of the ech42 transgene within the white spruce genome. The results suggest that the insertion and constitutive expression of the ech42 gene in white spruce did not significantly affect soil fungal biomass, diversity and community structure. © 2011 Her Majesty the Queen in Right of Canada FEMS Microbiology Ecology © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd.

Nematode diversity, abundance and community structure 50 years after the formation of the volcanic island of Surtsey

NASA Astrophysics Data System (ADS)

Ilieva-Makulec, K.; Bjarnadottir, B.; Sigurdsson, B. D.

2014-10-01

The soil nematode fauna can give important insights into soil development and other habitat changes that occur during primary succession. We investigated the generic composition, density, distribution and community structure of nematodes 50 years after the formation of a pristine volcanic island, Surtsey, Iceland. Part of the island has received additional nutrient inputs from seagulls breeding there since 1985, while the reminder has been much less affected and is at present found at a different successional sere. In total, 25 genera of nematodes were identified, of which 14 were reported on Surtsey for the first time. Nematode communities were more diverse in the more infertile area outside the gull colony, where 24 genera were found, compared to 18 inside. The trophic structure of the nematode communities showed relatively higher abundance of fungal feeders in the infertile areas, but relatively more bacterial- and plant-feeders inside the colony. Nematode abundance in surface soil was, however, significantly higher within the gull colony, with 16.7 ind. cm-2 compared to 3.6 ind. cm-2 outside. A multivariate analysis indicated that the nematode abundance and distribution on Surtsey were most strongly related to the soil C : N ratio, soil acidity, plant cover and biomass, soil temperature and soil depth.

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau

PubMed Central

Zhang, Kaoping; Shi, Yu; Jing, Xin; He, Jin-Sheng; Sun, Ruibo; Yang, Yunfeng; Shade, Ashley; Chu, Haiyan

2016-01-01

Soil microbial communities are influenced by climate change drivers such as warming and altered precipitation. These changes create abiotic stresses, including desiccation and nutrient limitation, which act on microbes. However, our understanding of the responses of microbial communities to co-occurring climate change drivers is limited. We surveyed soil bacterial and fungal diversity and composition after a 1-year warming and altered precipitation manipulation in the Tibetan plateau alpine grassland. In isolation, warming and decreased precipitation treatments each had no significant effects on soil bacterial community structure; however, in combination of both treatments altered bacterial community structure (p = 0.03). The main effect of altered precipitation specifically impacted the relative abundances of Bacteroidetes and Gammaproteobacteria compared to the control, while the main effect of warming impacted the relative abundance of Betaproteobacteria. In contrast, the fungal community had no significant response to the treatments after 1-year. Using structural equation modeling (SEM), we found bacterial community composition was positively related to soil moisture. Our results indicate that short-term climate change could cause changes in soil bacterial community through taxonomic shifts. Our work provides new insights into immediate soil microbial responses to short-term stressors acting on an ecosystem that is particularly sensitive to global climate change. PMID:27446064

Land use influences arbuscular mycorrhizal fungal communities in the farming-pastoral ecotone of northern China.

PubMed

Xiang, Dan; Verbruggen, Erik; Hu, Yajun; Veresoglou, Stavros D; Rillig, Matthias C; Zhou, Wenping; Xu, Tianle; Li, Huan; Hao, Zhipeng; Chen, Yongliang; Chen, Baodong

2014-12-01

We performed a landscape-scale investigation to compare the arbuscular mycorrhizal fungal (AMF) communities between grasslands and farmlands in the farming-pastoral ecotone of northern China. AMF richness and community composition were examined with 454 pyrosequencing. Structural equation modelling (SEM) and multivariate analyses were applied to disentangle the direct and indirect effects (mediated by multiple environmental factors) of land use on AMF. Land use conversion from grassland to farmland significantly reduced AMF richness and extraradical hyphal length density, and these land use types also differed significantly in AMF community composition. SEM showed that the effects of land use on AMF richness and hyphal length density in soil were primarily mediated by available phosphorus and soil structural quality. Soil texture was the strongest predictor of AMF community composition. Soil carbon, nitrogen and soil pH were also significantly correlated with AMF community composition, indicating that these abiotic variables could be responsible for some of the community composition differences among sites. Our study shows that land use has a partly predictable effect on AMF communities across this ecologically relevant area of China, and indicates that high soil phosphorus concentrations and poor soil structure are particularly detrimental to AMF in this fragile ecosystem. © 2014 The Author. New Phytologist © 2014 New Phytologist Trust.

Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient.

PubMed

Scola, Vincent; Ramond, Jean-Baptiste; Frossard, Aline; Zablocki, Olivier; Adriaenssens, Evelien M; Johnson, Riegardt M; Seely, Mary; Cowan, Don A

2018-01-01

The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.

Tellurium Distribution and Speciation in Contaminated Soils from Abandoned Mine Tailings: Comparison with Selenium.

PubMed

Qin, Hai-Bo; Takeichi, Yasuo; Nitani, Hiroaki; Terada, Yasuko; Takahashi, Yoshio

2017-06-06

The distribution and chemical species of tellurium (Te) in contaminated soil were determined by a combination of microfocused X-ray fluorescence (μ-XRF), X-ray diffraction (μ-XRD), and X-ray absorption fine structure (μ-XAFS) techniques. Results showed that Te was present as a mixture of Te(VI) and Te(IV) species, while selenium (Se) was predominantly present in the form of Se(IV) in the soil contaminated by abandoned mine tailings. In the contaminated soil, Fe(III) hydroxides were the host phases for Se(IV), Te(IV), and Te(VI), but Te(IV) could be also retained by illite. The difference in speciation and solubility of Se and Te in soil can result from different structures of surface complexes for Se and Te onto Fe(III) hydroxides. Furthermore, our results suggest that the retention of Te(IV) in soil could be relatively weaker than that of Te(VI) due to structural incorporation of Te(VI) into Fe(III) hydroxides. These findings are of geochemical and environmental significance for better understanding the solubility, mobility, and bioavailability of Te in the surface environment. To the best of our knowledge, this is the first study reporting the speciation and host phases of Te in field soil by the μ-XRF-XRD-XAFS techniques.

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau.

PubMed

Zhang, Kaoping; Shi, Yu; Jing, Xin; He, Jin-Sheng; Sun, Ruibo; Yang, Yunfeng; Shade, Ashley; Chu, Haiyan

2016-01-01

Soil microbial communities are influenced by climate change drivers such as warming and altered precipitation. These changes create abiotic stresses, including desiccation and nutrient limitation, which act on microbes. However, our understanding of the responses of microbial communities to co-occurring climate change drivers is limited. We surveyed soil bacterial and fungal diversity and composition after a 1-year warming and altered precipitation manipulation in the Tibetan plateau alpine grassland. In isolation, warming and decreased precipitation treatments each had no significant effects on soil bacterial community structure; however, in combination of both treatments altered bacterial community structure (p = 0.03). The main effect of altered precipitation specifically impacted the relative abundances of Bacteroidetes and Gammaproteobacteria compared to the control, while the main effect of warming impacted the relative abundance of Betaproteobacteria. In contrast, the fungal community had no significant response to the treatments after 1-year. Using structural equation modeling (SEM), we found bacterial community composition was positively related to soil moisture. Our results indicate that short-term climate change could cause changes in soil bacterial community through taxonomic shifts. Our work provides new insights into immediate soil microbial responses to short-term stressors acting on an ecosystem that is particularly sensitive to global climate change.

Bacterial community structure in the rhizosphere of a Cry1Ac Bt-brinjal crop and comparison to its non-transgenic counterpart in the tropical soil.

PubMed

Singh, Amit Kishore; Rai, Govind Kumar; Singh, Major; Dubey, Suresh Kumar

2013-11-01

To elucidate whether the transgenic crop alters the rhizospheric bacterial community structure, a 2-year study was performed with Cry1Ac gene-inserted brinjal crop (Bt) and their near isogenic non-transformed trait (non-Bt). The event of Bt crop (VRBT-8) was screened using an insect bioassay and enzyme-linked immunosorbent assay. Soil moisture, NH4 (+)-N, NO3 (-)-N, and PO4 (-)-P level had non-significant variation. Quantitative polymerase chain reaction revealed that abundance of bacterial 16S rRNA gene copies were lower in soils associated with Bt brinjal. Microbial biomass carbon (MBC) showed slight reduction in Bt brinjal soils. Higher MBC values in the non-Bt crop soil may be attributed to increased root activity and availability of readily metabolizable carbon compounds. The restriction fragment length polymorphism of PCR-amplified rRNA gene fragments detected 13 different bacterial groups with the exclusive presence of β-Proteobacteria, Chloroflexus, Planctomycetes, and Fusobacteria in non-Bt, and Cyanobacteria and Bacteroidetes in Bt soils, respectively, reflecting minor changes in the community structure. Despite the detection of Cry1Ac protein in the rhizospheric soil, the overall impact of Cry1Ac expressing Bt brinjal was less compared to that due to seasonal changes.

Changes of soil prokaryotic communities after clear-cutting in a karst forest: evidences for cutting-based disturbance promoting deterministic processes.

PubMed

Zhang, Xiao; Liu, Shirong; Li, Xiangzhen; Wang, Jingxin; Ding, Qiong; Wang, Hui; Tian, Chao; Yao, Minjie; An, Jiaxing; Huang, Yongtao

2016-03-01

To understand the temporal responses of soil prokaryotic communities to clear-cutting disturbance, we examined the changes in soil bacterial and archaeal community composition, structure and diversity along a chronosequence of forest successional restoration using high-throughput 16S rRNA gene sequencing. Our results demonstrated that clear-cutting significantly altered soil bacterial community structure, while no significant shifts of soil archaeal communities were observed. The hypothesis that soil bacterial communities would become similar to those of surrounding intact primary forest with natural regeneration was supported by the shifts in the bacterial community composition and structure. Bacterial community diversity patterns induced by clear-cutting were consistent with the intermediate disturbance hypothesis. Dynamics of bacterial communities was mostly driven by soil properties, which collectively explained more than 70% of the variation in bacterial community composition. Community assembly data revealed that clear-cutting promoted the importance of the deterministic processes in shaping bacterial communities, coinciding with the resultant low resource environments. But assembly processes in the secondary forest returned a similar level compared to the intact primary forest. These findings suggest that bacterial community dynamics may be predictable during the natural recovery process. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Community structure of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in soil treated with the insecticide imidacloprid.

PubMed

Cycoń, Mariusz; Piotrowska-Seget, Zofia

2015-01-01

The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the 10∗FR dosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4 (+), known as the most important factor which determines the contribution of these microorganisms to soil nitrification.

Community Structure of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria in Soil Treated with the Insecticide Imidacloprid

PubMed Central

Cycoń, Mariusz; Piotrowska-Seget, Zofia

2015-01-01

The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the 10∗FR dosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4 +, known as the most important factor which determines the contribution of these microorganisms to soil nitrification. PMID:25705674

Vegetation, soil, and flooding relationships in a blackwater floodplain forest

USGS Publications Warehouse

Burke, M.K.; King, S.L.; Gartner, D.; Eisenbies, M.H.

2003-01-01

Hydroperiod is considered the primary determinant of plant species distribution in temperate floodplain forests, but most studies have focused on alluvial (sediment-laden) river systems. Few studies have evaluated plant community relationships in blackwater river systems of the South Atlantic Coastal Plain of North America. In this study, we characterized the soils, hydroperiod, and vegetation communities and evaluated relationships between the physical and chemical environment and plant community structure on the floodplain of the Coosawhatchie River, a blackwater river in South Carolina, USA. The soils were similar to previous descriptions of blackwater floodplain soils but had greater soil N and P availability, substantially greater clay content, and lower soil silt content than was previously reported for other blackwater river floodplains. Results of a cluster analysis showed there were five forest communities on the site, and both short-term (4 years) and long-term (50 years) flooding records documented a flooding gradient: water tupelo community > swamp tupelo > laurel oak = overcup oak > mixed oak. The long-term hydrologic record showed that the floodplain has flooded less frequently from 1994 to present than in previous decades. Detrended correspondence analysis of environmental and relative basal area values showed that 27% of the variation in overstory community structure could be explained by the first two axes; however, fitting the species distributions to the DCA axes using Gaussian regression explained 67% of the variation. Axes were correlated with elevation (flooding intensity) and soil characteristics related to rooting volume and cation nutrient availability. Our study suggests that flooding is the major factor affecting community structure, but soil characteristics also may be factors in community structure in blackwater systems. ?? 2003, The Society of Wetland Scientists.

Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation.

PubMed

McGuire, Krista L; Fierer, Noah; Bateman, Carling; Treseder, Kathleen K; Turner, Benjamin L

2012-05-01

Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.

Insights from intercomparison of microbial and conventional soil models

NASA Astrophysics Data System (ADS)

Allison, S. D.; Li, J.; Luo, Y.; Mayes, M. A.; Wang, G.

2014-12-01

Changing the structure of soil biogeochemical models to represent coupling between microbial biomass and carbon substrate pools could improve predictions of carbon-climate feedbacks. So-called "microbial models" with this structure make very different predictions from conventional models based on first-order decay of carbon substrate pools. Still, the value of microbial models is uncertain because microbial physiological parameters are poorly constrained and model behaviors have not been fully explored. To address these issues, we developed an approach for inter-comparing microbial and conventional models. We initially focused on soil carbon responses to microbial carbon use efficiency (CUE) and temperature. Three scenarios were implemented in all models at a common reference temperature (20°C): constant CUE (held at 0.31), varied CUE (-0.016°C-1), and 50% acclimated CUE (-0.008°C-1). Whereas the conventional model always showed soil carbon losses with increasing temperature, the microbial models each predicted a temperature threshold above which warming led to soil carbon gain. The location of this threshold depended on CUE scenario, with higher temperature thresholds under the acclimated and constant scenarios. This result suggests that the temperature sensitivity of CUE and the structure of the soil carbon model together regulate the long-term soil carbon response to warming. Compared to the conventional model, all microbial models showed oscillatory behavior in response to perturbations and were much less sensitive to changing inputs. Oscillations were weakest in the most complex model with explicit enzyme pools, suggesting that multi-pool coupling might be a more realistic representation of the soil system. This study suggests that model structure and CUE parameterization should be carefully evaluated when scaling up microbial models to ecosystems and the globe.

[Effects of Organic and Inorganic Slow-Release Compound Fertilizer on Different Soils Microbial Community Structure].

PubMed

Wang, Fei; Yuan, Ting; Gu, Shou-kuan; Wang, Zheng-yin

2015-04-01

As a new style fertilizer, slow-control release fertilizer had been an important subject in recent years, but few researches were about soil microbial community structure diversity. Phospholipid fatty acid method was used to determined the microbial community structure diversity of acid soil and slight alkaline soil applied with slow-release compound fertilizer (SRF), chemical fertilizer (CF) and common compound fertilizer (CCF) at the 10th, 30th, 60th and 90th day under the constant temperature incubation condition. Results indicated that various bacteria (i. e 13:0, i14:0,14:0, i15:0, a15:0, i16:0, 16:12OH, 16:1w5c,16:0, i17:0, a17:0, cy17:0, 17:02OH, i18:0, 18:0 and cy19:0w8c), two actinomycetes (10Me17:0 and 10Me18:0) and only one fungus (18:1 w9c) were detected in two soils after applying slow-release compound fertilizer and other fertilizers during the whole incubation period. SRF could significantly increase the fungi PLFA content by 8.3% and 6.8% at the early stage (the 10th day and 30th day) compared with CF, as well as significantly increase by 22.7% and 17.1% at the late stage (the 60th day and 90th day) compared with CCF in acid soil. SRF significantly increased bacteria, fungi and gram positive bacteria compared with CF and CCF in incubation period (except at the 30th day) in slight alkaline soil. SRF could significantly improve the ratio of normal saturated fatty acid and monounsaturated fatty acid at the 30th day and 90th days in acid soil compared with no fertilizer (CK), CF and CCF, while as to slight alkaline soil, SRF was significantly greater than that of CK, CF and CCF only at the 60th day. SRF could significantly decrease the ratio of iso PLFA and anteiso PLFA in acid soil (in 30-90 days) and slight alkaline soil (in 10-60 days). For two soils PLFA varieties, contents and ratios of microbial community, slow-release compound fertilizer increased soil microbial PLFA varieties and contents, and decreased the influence to microbial survival environment, especially for the acid soil. Through the research of slow-release compound fertilizer on soil microbial community structure diversity, it could provide a scientific basis for widely application of slow-release compound fertilizer in agricultural production.

Soil Organic Matter in Its Native State: Unravelling the Most Complex Biomaterial on Earth.

PubMed

Masoom, Hussain; Courtier-Murias, Denis; Farooq, Hashim; Soong, Ronald; Kelleher, Brian P; Zhang, Chao; Maas, Werner E; Fey, Michael; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Simpson, Myrna J; Simpson, André J

2016-02-16

Since the isolation of soil organic matter in 1786, tens of thousands of publications have searched for its structure. Nuclear magnetic resonance (NMR) spectroscopy has played a critical role in defining soil organic matter but traditional approaches remove key information such as the distribution of components at the soil-water interface and conformational information. Here a novel form of NMR with capabilities to study all physical phases termed Comprehensive Multiphase NMR, is applied to analyze soil in its natural swollen-state. The key structural components in soil organic matter are identified to be largely composed of macromolecular inputs from degrading biomass. Polar lipid heads and carbohydrates dominate the soil-water interface while lignin and microbes are arranged in a more hydrophobic interior. Lignin domains cannot be penetrated by aqueous solvents even at extreme pH indicating they are the most hydrophobic environment in soil and are ideal for sequestering hydrophobic contaminants. Here, for the first time, a complete range of physical states of a whole soil can be studied. This provides a more detailed understanding of soil organic matter at the molecular level itself key to develop the most efficient soil remediation and agricultural techniques, and better predict carbon sequestration and climate change.

Effect of Activated Carbon Amendment on Bacterial Community Structure and Functions in a PAH Impacted Urban Soil

PubMed Central

2012-01-01

We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. PMID:22455603

Effects of reclamation years on composition and diversity of soil bacterial communities in Northwest China.

PubMed

Cheng, Zhibo; Zhang, Fenghua; Gale, William Jeffrey; Wang, Weichao; Sang, Wen; Yang, Haichang

2018-01-01

The objective of this study was to evaluate bacterial community structure and diversity in soil aggregate fractions when salinized farmland was reclaimed after >27 years of abandonment and then farmed again for 1, 5, 10, and 15 years. Illumina MiSeq high-throughput sequencing was performed to characterize the soil bacterial communities in 5 aggregate size classes in each treatment. The results indicated that reclamation significantly increased macro-aggregation (>0.25 mm), as well as soil organic C, available N, and available P. The 10-year field had the largest proportion (93.9%) of soil in the macro-aggregate size classes (i.e., >0.25 mm) and the highest soil electrical conductivity. The 5 most dominant phyla in the soil samples were Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria, and Bacteroidetes. The phylogenetic diversity, Chao1, and Shannon indices increased after the abandoned land was reclaimed for farming, reaching maximums in the 15-year field. Among aggregate size classes, the 1-0.25 mm aggregates generally had the highest phylogenetic diversity, Chao1, and Shannon indices. Soil organic C and soil electrical conductivity were the main environmental factors affecting the soil bacterial communities. The composition and structure of the bacterial communities also varied significantly depending on soil aggregate size and time since reclamation.

Complex Forms of Soil Organic Phosphorus-A Major Component of Soil Phosphorus.

PubMed

McLaren, Timothy I; Smernik, Ronald J; McLaughlin, Mike J; McBeath, Therese M; Kirby, Jason K; Simpson, Richard J; Guppy, Christopher N; Doolette, Ashlea L; Richardson, Alan E

2015-11-17

Phosphorus (P) is an essential element for life, an innate constituent of soil organic matter, and a major anthropogenic input to terrestrial ecosystems. The supply of P to living organisms is strongly dependent on the dynamics of soil organic P. However, fluxes of P through soil organic matter remain unclear because only a minority (typically <30%) of soil organic P has been identified as recognizable biomolecules of low molecular weight (e.g., inositol hexakisphosphates). Here, we use (31)P nuclear magnetic resonance spectroscopy to determine the speciation of organic P in soil extracts fractionated into two molecular weight ranges. Speciation of organic P in the high molecular weight fraction (>10 kDa) was markedly different to that of the low molecular weight fraction (<10 kDa). The former was dominated by a broad peak, which is consistent with P bound by phosphomonoester linkages of supra-/macro-molecular structures, whereas the latter contained all of the sharp peaks that were present in unfractionated extracts, along with some broad signal. Overall, phosphomonoesters in supra-/macro-molecular structures were found to account for the majority (61% to 73%) of soil organic P across the five diverse soils. These soil phosphomonoesters will need to be integrated within current models of the inorganic-organic P cycle of soil-plant terrestrial ecosystems.

Effect of activated carbon amendment on bacterial community structure and functions in a PAH impacted urban soil.

PubMed

Meynet, Paola; Hale, Sarah E; Davenport, Russell J; Cornelissen, Gerard; Breedveld, Gijs D; Werner, David

2012-05-01

We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. © 2012 American Chemical Society

Development of soils and communities of plants and arbuscular mycorrhizal fungi on West Virginia surface mines.

PubMed

Levy, Michael A; Cumming, Jonathan R

2014-11-01

Surface mining followed by reclamation to pasture is a major driver of land use and cover change in Appalachia. Prior research suggests that many aspects of ecosystem recovery are either slow or incomplete. We examined ecosystem structure-including soil physical and chemical properties, arbuscular mycorrhizal fungal (AMF) infectivity and community composition, and plant diversity and community composition-on a chronosequence of pasture-reclaimed surface mines and a non-mined pasture in northern West Virginia. Surface mining and reclamation dramatically altered ecosystem structure. Some aspects of ecosystem structure, including many measures of soil chemistry and infectivity of AMF, returned rapidly to levels found on the non-mined reference site. Other aspects of ecosystem structure, notably soil physical properties and AMF and plant communities, showed incomplete or no recovery over the short-to-medium term. In addition, invasive plants were prevalent on reclaimed mine sites. The results point to the need for investigation on how reclamation practices could minimize establishment of exotic invasive plant species and reduce the long-term impacts of mining on ecosystem structure and function.

Bringing life to soil physical processes

NASA Astrophysics Data System (ADS)

Hallett, P. D.

2013-12-01

When Oklahoma's native prairie grass roots were replaced by corn, the greatest environmental (and social) disaster ever to hit America ensued. The soils lost structure, physical binding by roots was annihilated and when drought came the Great Dust Bowl commenced. This form of environmental disaster has repeated over history and although not always apparent, similar processes drive the degradation of seemingly productive farmland and forests. But just as negative impacts on biology are deleterious to soil physical properties, positive impacts could reverse these trends. In finding solutions to soil sustainability and food security, we should be able to exploit biological processes to improve soil physical properties. This talk will focus on a quantitative understanding of how biology changes soil physical behaviour. Like the Great Dust Bowl, it starts with reinforcement mechanisms by plant roots. We found that binding of soil by cereal (barley) roots within 5 weeks of planting can more than double soil shear strength, with greater plant density causing greater reinforcement. With time, however, the relative impact of root reinforcement diminishes due to root turnover and aging of the seedbed. From mechanical tests of individual roots, reasonable predictions of reinforcement by tree roots are possible with fibre bundle models. With herbaceous plants like cereals, however, the same parameters (root strength, stiffness, size and distribution) result in a poor prediction. We found that root type, root age and abiotic factors such as compaction and waterlogging affect mechanical behaviour, further complicating the understanding and prediction of root reinforcement. For soil physical stability, the interface between root and soil is an extremely important zone in terms of resistance of roots to pull-out and rhizosphere formation. Compounds analogous to root exudates have been found with rheological tests to initially decrease the shear stress where wet soils flow, but after decomposition of these exudates by microbes the shear stress increases. This suggests an initial dispersion, followed by aggregation of the soil, which explains the structural arrangement of soil particles in the rhizosphere observed by microscopy. Dispersion of soil minerals in the root zone is important to release bound nutrients from mineral surfaces. Using fracture mechanics we measured large impacts of biological exudates on the toughness and interparticle bond energy of soils. Now novel tests are being developed to quantify interparticle bonding by biological exudates on single and multiple particle contacts, including mechanical test specimens that can be inoculated with specific bacteria or fungi. This will allow for clay mineralogy, water potential and solution chemistry impacts on interparticle bonding to be quantified directly. Wettability experiments with the same samples measure hydrological properties such as contact angle. Basic information from these tests will help explain biological processes that drive soil structure formation and stabilisation, providing data for models of soil structure dynamics.

Four millennia of woodland structure and dynamics at the Arctic treeline of eastern Canada.

PubMed

Auger, Sarah; Payette, Serge

2010-05-01

Paleoecological analysis using complementary indicators of vegetation and soil can provide spatially explicit information on ecological processes influencing trajectories of long-term ecosystem change. Here we document the structure and dynamics of an old-growth woodland before and after its inception 1000 years ago. We infer vegetation and soil characteristics from size and age distributions of black spruce (Picea mariana (Mill.) B.S.P.), soil properties, plant fossils, and paleosols. Radiocarbon ages of charcoal on the ground and in the soil indicate that the fire return interval was approximately 300 years between 2750 and 1000 cal. yr BP. No fire evidence was found before and after this period despite the presence of spruce since 4200 cal. yr BP. The size structures of living and dead spruce suggest that the woodland is in equilibrium with present climate in absence of fire. Tree establishment and mortality occurred regularly since the last fire event around 950 cal. yr BP. Both layering and occasional seeding have contributed to stabilize the spatial distribution of spruce over the past 1000 years. Since initial afforestation, soil development has been homogenized by the changing spatial distribution of spruce following each fire. We conclude that the history of the woodland is characterized by vegetation shifts associated with fire and soil disturbances and by millennial-scale maintenance of the woodland's structure despite changing climatic conditions.

Comparative study of rhizobacterial community structure of plant species in oil-contaminated soil.

PubMed

Lee, Eun-Hee; Cho, Kyong-Suk; Kim, Jaisoo

2010-09-01

In this study, the identity and distribution of plants and the structure of their associated rhizobacterial communities were examined in an oil-contaminated site. The number of plant species that formed a community or were scattered was 24. The species living in soil highly contaminated with total petroleum hydrocarbon (TPH) (9,000-4,5000 mg/g-soil) were Cynodon dactylon, Persicaria lapathifolia, and Calystegia soldanella (a halophytic species). Among the 24 plant species, the following have been known to be effective for oil removal: C. dactylon, Digitaria sanguinalis, and Cyperus orthostachyus. Denaturing gradient gel electrophoresis (DGGE) profile analysis showed that the following pairs of plant species had highly similar (above 70%) rhizobacterial community structures: Artemisia princeps and Hemistepta lyrata; C. dactylon and P. lapathifolia; Carex kobomugi and Cardamine flexuosa; and Equisetum arvense and D. sanguinalis. The major groups of rhizobacteria were Betaproteobacteria, Gamma-proteobacteria, Chloroflexi, Actinobacteria, and unknown. Based on DGGE analysis, P. lapathifolia, found for the first time in this study growing in the presence of high TPH, may be a good species for phytoremediation of oil-contaminated soils and in particular, C. soldanella may be useful for soils with high TPH and salt concentrations. Overall, this study suggests that the plant roots, regardless of plant species, may have a similar influence on the bacterial community structure in oil-contaminated soil.

Soil-borne microbial functional structure across different land uses.

PubMed

Kuramae, Eiko E; Zhou, Jizhong Z; Kowalchuk, George A; van Veen, Johannes A

2014-01-01

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

Effect of Inoculation of Acacia senegal mature trees with Mycorrhiza and Rhizobia on soil properties and microbial community structure

NASA Astrophysics Data System (ADS)

Assigbetsé, K.; Ciss, I.; Bakhoum, N.; Dieng, L.

2012-04-01

Inoculation of legume plants with symbiotic microorganisms is widely used to improve their development and productivity. The objective of this study was to investigate the effect of inoculation of Acacia senegal mature trees with rhizobium (Sinorhizobium) and arbuscular mycorrhizal fungus (G. mosseae, G. fasciculatum, G. intraradices) either singly or in combination, on soil properties, activity and the genetic structure of soil microbial communities. The experiment set up in Southern Senegal consisted of 4 randomized blocks of A. senegal mature trees with 4 treatments including inoculated trees with Rhizobium (R), mycorrhizal fungus (M) and with Rhizobium+mycorhizal fungus (RM) and non-inoculated control (CON). Soil were sampled 2 years after the inoculation. Soil pH, C and N and available P contents were measured. The microbial abundance and activity were measured in terms of microbial biomass C (MBC) and basal soil respiration. The community structure of the total bacterial, diazotrophic and denitrifying communities was assessed by denaturing gradient gel electrophoresis of 16S rDNA, nifH and nirK genes respectively. Inoculations with symbiont under field conditions have increased soil pH. The C and N contents were enhanced in the dual-inoculated treatments (RM). The mycorrhized treatment have displayed the lowest available P contents while RM and R treatments exhibited higher contents rates. The microbial biomass C rates were higher in treatments co-inoculated with AM fungi and Rhizobium than in those inoculated singly with AM fungi or Rhizobium strains. The basal soil respiration were positively correlated to MBC, and the highest rates were found in the co-inoculated treatments. Fingerprints of 16S rDNA gene exhibited similar patterns between inoculated treatments and the control showing that the inoculation of mature trees have not impacted the total bacterial community structure. In contrast, the inoculated treatments have displayed individually different diazotrophic and denitrifying communities fingerprints, indicating that the inoculation with microsymbionts have modified the genetic structure of the two functional communities in soil. Further, the diazotrophic community richness was reduced over the control indicating the impact of the addition of symbionts on the free-living N2-fixing bacterial (nifH) diversity. This study shows that inoculation of A. senegal mature trees with rhizobium and arbuscular mycorrhizal fungus has enhanced soil biofunctioning and modified the genetic structure of microbial community involved in N-cycling. Combined inoculation of AM fungi and Rhizobium have improved these effects on chemical characteristics, microbial community abundance and activity demonstrating synergism between the two microsymbionts.

A dynamic organic soil biogeochemical model for simulating the effects of wildfire on soil environmental conditions and carbon dynamics of black spruce forests

Treesearch

Shuhua Yi; A. David McGuire; Eric Kasischke; Jennifer Harden; Kristen Manies; Michelle Mack; Merritt Turetsky

2010-01-01

Ecosystem models have not comprehensively considered how interactions among fire disturbance, soil environmental conditions, and biogeochemical processes affect ecosystem dynamics in boreal forest ecosystems. In this study, we implemented a dynamic organic soil structure in the Terrestrial Ecosystem Model (DOS-TEM) to investigate the effects of fire on soil temperature...

Soil macroinvertebrate communities across a productivity gradient in deciduous forests of eastern North America

Treesearch

Evelyn S. Wenk; Mac A. Callaham; Joseph O' Brien; Paul J. Hanson

2016-01-01

Within the temperate, deciduous forests of the eastern US, diverse soil-fauna communities are structured by a combination of environmental gradients and interactions with other biota. The introduction of non-native soil taxa has altered communities and soil processes, and adds another degree of variability to these systems. We sampled soil macroinvertebrate abundance...

Compositional changes of soil organic matter with cropping time were more profound in subsoils and distinct between Phaeozem and Chernozem in Northeast China

USDA-ARS?s Scientific Manuscript database

Soil organic matter (SOM) contributes to soil processes and is found both in shallow and deep soil layers. Its activity can be affected by its chemical composition, yet knowledge is incomplete of how land use alters the structural composition of SOM throughout the profiles of different soil types. T...

Do anaerobic digestates promote dispersion, acidification and water repellency in soils?

NASA Astrophysics Data System (ADS)

Voelkner, Amrei; Holthusen, Dörthe; Horn, Rainer

2014-05-01

Digestates are used as organic fertilizer on agricultural land due to their high amounts of nutrients (e.g. potassium, sodium). It is commonly expected that the application of sludge derived from anaerobic digestion can influence the soil structure and soil stability. Due to the fact that digestates contain large quantities of monovalent salts and long-chained fatty acids, the consequence of sludge amendment can be soil degradation caused by acidification, dispersion and increased water-repellency. Thus, water infiltration can be impeded which results in a preservation of stable soil aggregates. However, a diminished water infiltration can support water erosion and preferential flow of easy soluble nutrients into the groundwater. Our research was conducted with different digestates derived from maize, wheat and sugar beet to examine occurring processes in soils of two different textures after the application of anaerobic sludges. Particularly, we focused on the wetting properties of the soil. For this purpose, the wetting behavior was investigated by determining the sorptivity-based Repellency Index with moist samples and the contact angle with homogenized, air-dried soil material. Further surveys were carried out to assess the flow behavior of digestates application and the deformation of the particle-to-particle association by microscaled shearing. Additionally, the acidification process in the soil as a result of sludge application was investigated. To account for the dispersive impact of digestates, the turbidity of soil suspensions was ascertained. We summarize from the results that the digestates have a clear impact on the water repellency of the soil. We recognized a shift to more hydrophobic conditions. Partially, the pH remains on a high level due to the alkaline digestate, but several samples show a decline of pH, depending on the soil texture, respectively. However, soil structure was weakened as was shown by an increase of turbidity. As a conclusion, we point out the necessity to take into account the impact which anaerobic digestates might have on soil structure and stability in addition to their fertilizing effect to sustain the soil in a good state.

Reappraisal of soil C storage processes. The controversy on structural diversity of humic substances as biogeochemical driver for soil C fluxes

NASA Astrophysics Data System (ADS)

Almendros, Gonzalo; Gonzalez-Vila, Francisco J.; Gonzalez-Perez, Jose Antonio; Knicker, Heike

2016-04-01

The functional relationships between the macromolecular structure of the humic substances (HS) and a series of biogeochemical processes related with the C sequestration performance in soils have been recently questioned. In this communication we collect recent data from a wide array of different ecosystems where the C storage in soils has been studied and explained as a possible cause-to-effect relationship or has been found significantly correlated (multivariate statistical models) with a series of structural characteristics of humic materials. The study of humic materials has methodological analytical limitations that are derived from its complex, chaotic and not completely understood structure, that reflects its manifold precursors as well as the local impact of environmental/depositional factors. In this work we attempt to design an exploratory, multiomic approach based on the information provided by the molecular characterization of the soil organic matter (SOM). Massive data harvesting was carried out of statistical variables, to infer biogeochemical proxies (spectroscopic, chromatographic, mass spectrometric quantitative descriptors). The experimental data were acquired from advanced instrumental methodologies, viz, analytical pyrolysis, compound-specific stable isotope analysis (CSIA), derivative infrared (FTIR) spectroscopy, solid-state C-13 and N-15 nuclear magnetic resonance (NMR) and mass spectrometry (MS) data after direct injection (thermoevaporation), previous pyrolysis, or ion averaging of specific m/z ranges from classical GC/MS chromatograms. In the transversal exploratory analysis of the multianalytical information, the data were coded for on-line processing in a stage in which there is no need for interpretation, in molecular or structural terms, of the quantitative data consisting of e.g., peak intensities, signal areas, chromatographic (GC) total abundances, etc. A series of forecasting chemometric approaches (aiming to express SOM biodegradability, or soil C resilience as a function of intrinsic molecular characteristics of the SOM) were especially successful in the case of: a) linear multiple regression models (LMR) with automatic backward variable selection, b) supervised removal of internal redundancy of the variables based on multidimensional scaling (MDS), and c) partial least squares (PLS) regression to obtain the variable importance for projection (VIP) which is useful to identify new environmental proxies. At least the results obtained from differing continental Mediterranean soils showed that a large influence of local (soil-dependant) abiotic factors in the final variance (of the total soil C quality and quantity) was explained by the SOM molecular structure. This conclusion is relevant as regards the recent (in our opinion hermeneutic and speculative) controversy disregarding the importance of the structural features of HS in biogeochemical and environmental processes controlling C sequestration in soils.

Effect of the historical land use on the structure of forest soils in European Russia

NASA Astrophysics Data System (ADS)

Bobrovskii, M. V.

2010-12-01

The morphological structure of the soils in the forest areas of European Russia was analyzed. It was shown that most of the soils were formed under the impact of both biotic and anthropogenic factors. Soils with poorly differentiated profiles without podzolization features are typical for the least disturbed forest ecosystems. The presence of an eluvial (EL) horizon is associated with the signs of old plowing and (or) fires. The character and rate of the soil cover transformation under various impacts of the historical land use (felling, plowing, pasturing, burning, etc.) are discussed. The technologies of the main traditional farming systems in the forest zone of European Russia (slash-and-burn, fallow, and shifting farming systems) are considered; their effect on the long-term dynamics of the soil cover is estimated. Farming and the related impacts of historical land use can be a major reason for the formation of degraded soils in the forest zone of European Russia.

Comparison of phytoremediation potential capacity of Spartina densiflora and Sarcocornia perennis for metal polluted soils.

PubMed

Idaszkin, Yanina L; Lancelotti, Julio L; Pollicelli, María P; Marcovecchio, Jorge E; Bouza, Pablo J

2017-05-15

Phytoremediation is considered the most appropriate technique to restore metal polluted soil, given its low cost, high efficiency and low environmental impact. Spartina densiflora and Sarcocornia perennis are perennial halophytes growing under similar environmental conditions in San Antonio marsh (Patagonia Argentina), therefore it is interesting to compare their phytoremediation potential capacity. To this end, we compared concentrations of Pb, Zn, Cu, and Fe in soils and in below- and above-ground structures of S. perennis and S. densiflora. It was concluded that both species are able to inhabit Pb, Zn, and Cu polluted soils. Although Sarcocornia translocated more metals to the aerial structures than Spartina, both species translocated only when they were growing in soils with low metal concentrations. It seems that the plants translocate only a certain proportion of the metal contained in the soil. These results suggest that both species could be considered candidates to phytostabilize these metals in polluted soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Freeze-Thaw Cycles Effects on Soil Compaction in a Clay Loam

NASA Astrophysics Data System (ADS)

Jabro, J.; Evans, R.; Iversen, W.

2012-04-01

Inappropriate soil management practices and heavier farm machinery and equipment have led to an increase in soil compaction in the last two decades prompting increased global concern regarding the impact of soil compaction on crop production and soil quality in modern mechanized agriculture. A 3-yr comprehensive study was established to evaluate the dynamic of freeze-thaw cycles on soil compaction in a clay loam soil. Plots of frozen soils were compared with plots where soils were prevented from freezing with electrically heated blankets commonly used on concrete. Results showed that frequent freeze-thaw cycles over the winter alleviated a majority of soil compaction at the 0 - 20 cm depth. Soil penetration resistance in compacted soils was reduced by 73 and 68% over the winter at the 0 - 10 and 10 - 20 cm depths, respectively, due to dynamic effects of freeze-thaw cycles on soil structure and particles configuration. In unfrozen compacted soils, the penetration resistance was also reduced by 50 and 60% over winter at the 0 - 10 and 10 - 20 cm depths, respectively, due to the biology of soil, microbial activity, and disruptive effects of shrink-swell cycles. These results have demonstrated of how repeated freeze-thaw cycles can alleviate soil compaction, alter soil physical quality and create optimal soil conditions required for profitable growth of agricultural crops. The results from this study will save growers considerable time, money and energy currently required to alleviate soil compaction using other methods such as sub-soiling and deep tillage. We believe that Mother Nature provides ways to reverse soil compaction and improve soil structure and aggregation through the dynamic of freeze-thaw cycles that soils in Montana and other parts of the country go through each year. We concluded that the Mother Nature is the most effective and cheapest way to alleviate soil compaction.